Variant report

Variant	rs34416404
Chromosome Location	chr6:31782544-31782545
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr6:31782320-31782669	GM12878	blood:	n/a	chr6:31782466-31782476 chr6:31782459-31782473
2	POLR2A	chr6:31782497-31782791	HepG2	liver:	n/a	n/a
3	YY1	chr6:31782410-31782665	GM12892	blood:	n/a	chr6:31782506-31782518 chr6:31782507-31782529
4	E2F6	chr6:31782290-31782596	K562	blood:	n/a	chr6:31782493-31782502 chr6:31782467-31782476
5	HCFC1	chr6:31781524-31783637	Hela-S3	cervix:	n/a	n/a
6	STAT3	chr6:31782214-31782721	MCF10A-Er-Src	breast:	n/a	chr6:31782467-31782479 chr6:31782457-31782469
7	CREB1	chr6:31782283-31783609	K562	blood:	n/a	n/a
8	CEBPD	chr6:31782355-31783736	K562	blood:	n/a	n/a
9	MXI1	chr6:31782436-31783545	HepG2	liver:	n/a	chr6:31783043-31783058
10	POLR2A	chr6:31782278-31782795	K562	blood:	n/a	n/a
11	CCNT2	chr6:31782213-31783707	K562	blood:	n/a	chr6:31782769-31782778
12	RUNX3	chr6:31782317-31782820	GM12878	blood:	n/a	n/a
13	MAFK	chr6:31782464-31783547	K562	blood:	n/a	n/a
14	IRF1	chr6:31782203-31783561	K562	blood:	n/a	n/a
15	SP1	chr6:31782259-31782768	A549	lung:	n/a	chr6:31782531-31782542 chr6:31782466-31782480 chr6:31782467-31782476
16	POLR2A	chr6:31782248-31783574	K562	blood:	n/a	n/a
17	POLR2A	chr6:31782256-31782781	ProgFib	skin:	n/a	n/a
18	POLR2A	chr6:31782425-31784264	A549	lung:	n/a	n/a
19	POLR2A	chr6:31782314-31782799	U87	brain:	n/a	n/a
20	RELA	chr6:31782439-31782795	GM18951	blood:	n/a	n/a
21	SRF	chr6:31782386-31782895	ECC-1	luminal epithelium:	n/a	chr6:31782605-31782622 chr6:31782604-31782617 chr6:31782602-31782620
22	POLR2A	chr6:31782489-31782721	A549	lung:	n/a	n/a
23	TAF1	chr6:31782440-31782768	Hela-S3	cervix:	n/a	n/a
24	NFYB	chr6:31782358-31783529	K562	blood:	n/a	chr6:31783248-31783258 chr6:31783165-31783177 chr6:31783161-31783176 chr6:31783249-31783261 chr6:31783161-31783176 chr6:31783245-31783260 chr6:31783163-31783178 chr6:31783164-31783174 chr6:31783245-31783260 chr6:31783162-31783176 chr6:31782491-31782504
25	POLR2A	chr6:31782396-31782761	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:31782195-31783574	K562	blood:	n/a	n/a
27	PBX3	chr6:31782287-31782590	A549	lung:	n/a	chr6:31782494-31782505
28	STAT1	chr6:31782482-31782791	GM12878	blood:	n/a	chr6:31782777-31782789
29	POLR2A	chr6:31782438-31782756	HepG2	liver:	n/a	n/a
30	HEY1	chr6:31782516-31782712	HepG2	liver:	n/a	n/a
31	NANOG	chr6:31782367-31782687	H1-hESC	embryonic stem cell:	n/a	n/a
32	RCOR1	chr6:31782357-31783517	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr6:31782485-31783547	K562	blood:	n/a	n/a
34	POLR2A	chr6:31782439-31782760	GM12892	blood:	n/a	n/a
35	TAF1	chr6:31782365-31783832	H1-hESC	embryonic stem cell:	n/a	n/a
36	YY1	chr6:31782278-31782737	ECC-1	luminal epithelium:	n/a	chr6:31782506-31782518 chr6:31782507-31782529
37	EP300	chr6:31782370-31782712	SK-N-SH_RA	brain:	n/a	chr6:31782372-31782385 chr6:31782453-31782466
38	POLR2A	chr6:31781969-31783588	K562	blood:	n/a	n/a
39	MAX	chr6:31782320-31783603	A549	lung:	n/a	chr6:31783047-31783056 chr6:31782900-31782910 chr6:31783079-31783089
40	MAX	chr6:31782299-31783598	MCF-7	breast:	n/a	chr6:31783047-31783056 chr6:31782900-31782910 chr6:31783079-31783089
41	MYC	chr6:31782322-31782784	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr6:31782384-31783571	Hela-S3	cervix:	n/a	n/a
43	CHD2	chr6:31782382-31782749	GM12878	blood:	n/a	n/a
44	SIN3AK20	chr6:31782271-31783630	PANC-1	pancreas:	n/a	n/a
45	YY1	chr6:31782359-31782747	A549	lung:	n/a	chr6:31782506-31782518 chr6:31782507-31782529
46	FOXA1	chr6:31782425-31782704	T-47D	breast:	n/a	n/a
47	POLR2A	chr6:31782226-31782743	HCT-116	colon:	n/a	n/a
48	POLR2A	chr6:31782226-31783577	K562	blood:	n/a	n/a
49	POLR2A	chr6:31782435-31782892	GM12892	blood:	n/a	n/a
50	CHD2	chr6:31782419-31782574	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31781796..31783894-chr6:31925428..31927086,2	K562	blood:
2	chr6:31781417..31783934-chr6:32937499..32939420,2	K562	blood:
3	chr2:96810724..96811482-chr6:31782507..31783438,2	Hela-S3	cervix:
4	chr6:31780821..31784746-chr6:31829825..31831701,4	MCF-7	breast:
5	chr6:31507867..31510784-chr6:31781026..31784406,3	MCF-7	breast:
6	chr6:31782095..31783822-chr6:31794892..31795963,5	MCF-7	breast:
7	chr6:31782025..31784864-chr6:32163977..32165547,2	K562	blood:
8	chr6:31781780..31785433-chr6:31828310..31832689,5	K562	blood:
9	chr6:31513245..31516542-chr6:31782394..31785632,3	MCF-7	breast:
10	chr6:31780396..31783150-chr6:32157710..32160077,2	K562	blood:
11	chr6:31781780..31785433-chr6:31829263..31832689,6	K562	blood:
12	chr6:31743107..31747994-chr6:31781956..31785553,7	MCF-7	breast:
13	chr6:31587709..31590301-chr6:31782411..31784104,4	MCF-7	breast:
14	chr6:31780956..31783456-chr6:31865283..31866829,2	K562	blood:
15	chr6:31780296..31786175-chr6:31828333..31833086,7	MCF-7	breast:
16	chr6:31782320..31783797-chr6:31794894..31795956,19	Hela-S3	cervix:
17	chr6:31759482..31765185-chr6:31781824..31784897,13	MCF-7	breast:
18	chr6:31756951..31764627-chr6:31780500..31799197,32	MCF-7	breast:
19	chr19:18391974..18392588-chr6:31782500..31783099,2	Hela-S3	cervix:
20	chr6:31508732..31511014-chr6:31781931..31784408,2	K562	blood:
21	chr6:31781258..31784668-chr6:32935964..32938963,3	MCF-7	breast:
22	chr6:31781426..31784987-chr6:31937458..31940746,3	K562	blood:
23	chr6:31780574..31784383-chr6:31865157..31867218,4	K562	blood:

Variant related genes	Relation type
HSPA1A	TF binding region
ENSG00000213760	Chromatin interaction
ENSG00000204351	Chromatin interaction
ENSG00000204356	Chromatin interaction
ENSG00000265236	Chromatin interaction
ENSG00000201555	Chromatin interaction
ENSG00000158050	Chromatin interaction
ENSG00000204394	Chromatin interaction
ENSG00000204301	Chromatin interaction
ENSG00000204344	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000204396	Chromatin interaction
ENSG00000204348	Chromatin interaction
ENSG00000204385	Chromatin interaction
ENSG00000204386	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000204304	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000234006	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11965654	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11966331	0.85[AFR][1000 genomes]
rs13193280	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17207552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17207622	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713489	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4947332	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59324322	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
10	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
11	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases
13	nsv884426	chr6:31728102-31800868	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
14	nsv884427	chr6:31728102-31802465	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
15	nsv884428	chr6:31728102-31870326	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
16	nsv884429	chr6:31730356-31837066	Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
17	nsv884430	chr6:31731881-31800631	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
18	nsv462872	chr6:31778272-31864304	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
19	nsv601945	chr6:31778272-31864304	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
20	nsv981359	chr6:31779004-31797103	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
21	nsv869989	chr6:31779203-31797657	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	114 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31774800-31782600	Weak transcription	Lung	lung
2	chr6:31774800-31783000	Weak transcription	Gastric	stomach
3	chr6:31781400-31783400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr6:31781600-31782800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr6:31781600-31782800	Active TSS	Right Atrium	heart
6	chr6:31781600-31783000	Active TSS	Colonic Mucosa	Colon
7	chr6:31781600-31783600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:31781600-31783600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr6:31781600-31783800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr6:31781600-31783800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:31781600-31783800	Active TSS	Fetal Brain Female	brain
12	chr6:31781600-31783800	Active TSS	Left Ventricle	heart
13	chr6:31781600-31783800	Active TSS	Right Ventricle	heart
14	chr6:31781800-31782600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:31781800-31782600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:31781800-31782600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:31781800-31782600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:31781800-31782600	Weak transcription	Aorta	Aorta
19	chr6:31781800-31783600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:31781800-31783600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:31781800-31783600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:31781800-31783600	Active TSS	Brain Angular Gyrus	brain
23	chr6:31781800-31783600	Active TSS	Brain Substantia Nigra	brain
24	chr6:31781800-31783600	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr6:31781800-31783600	Active TSS	Ovary	ovary
26	chr6:31781800-31783600	Active TSS	NHLF	lung
27	chr6:31781800-31783800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr6:31781800-31783800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:31781800-31783800	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr6:31781800-31783800	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr6:31781800-31783800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:31781800-31783800	Active TSS	Brain Anterior Caudate	brain
33	chr6:31781800-31783800	Active TSS	Brain Germinal Matrix	brain
34	chr6:31781800-31783800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:31781800-31783800	Active TSS	Fetal Kidney	kidney
36	chr6:31781800-31783800	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr6:31781800-31783800	Active TSS	Rectal Smooth Muscle	rectum
38	chr6:31781800-31783800	Active TSS	K562	blood
39	chr6:31782000-31782600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:31782000-31782600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:31782000-31782600	Weak transcription	Small Intestine	intestine
42	chr6:31782000-31782600	Enhancers	Stomach Mucosa	stomach
43	chr6:31782000-31782600	Weak transcription	Spleen	Spleen
44	chr6:31782000-31782600	Enhancers	HMEC	breast
45	chr6:31782000-31782600	Enhancers	HUVEC	blood vessel
46	chr6:31782000-31782600	Enhancers	NH-A	brain
47	chr6:31782000-31782600	Weak transcription	NHDF-Ad	bronchial
48	chr6:31782000-31782800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:31782000-31782800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:31782000-31782800	Enhancers	Fetal Heart	heart

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