Variant report

Variant	rs368210
Chromosome Location	chr3:51976294-51976295
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	SIN3AK20	chr3:51975610-51976498	HepG2	liver:	n/a	n/a
2	JUND	chr3:51976015-51976412	HepG2	liver:	n/a	n/a
3	E2F6	chr3:51975754-51976595	A549	lung:	n/a	chr3:51976079-51976088 chr3:51976000-51976009 chr3:51976164-51976173 chr3:51976404-51976414
4	ELK1	chr3:51976002-51976379	K562	blood:	n/a	n/a
5	FOS	chr3:51975865-51976358	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr3:51976048-51976345	ECC-1	luminal epithelium:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
7	RAD21	chr3:51976063-51976434	A549	lung:	n/a	chr3:51976332-51976345 chr3:51976232-51976251 chr3:51976101-51976115
8	CTCF	chr3:51976160-51976310	GM12873	blood:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
9	MAX	chr3:51975537-51976634	H1-hESC	embryonic stem cell:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
10	KAP1	chr3:51975914-51976565	HEK293	kidney:	n/a	chr3:51976208-51976216
11	CUX1	chr3:51976222-51976972	GM12878	blood:	n/a	n/a
12	CTCF	chr3:51976102-51976373	HUVEC	blood vessel:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
13	HCFC1	chr3:51974752-51977446	Hela-S3	cervix:	n/a	n/a
14	RELA	chr3:51975696-51977084	GM18951	blood:	n/a	n/a
15	CTCF	chr3:51976160-51976310	GM12871	blood:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
16	USF2	chr3:51975781-51976544	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAZ	chr3:51975614-51977420	Hela-S3	cervix:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
18	POLR2A	chr3:51975661-51976598	H1-neurons	neurons:	n/a	n/a
19	TEAD4	chr3:51976031-51976484	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr3:51976160-51976310	AoAF	blood vessel:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
21	IRF1	chr3:51975745-51976446	K562	blood:	n/a	chr3:51976075-51976089 chr3:51976038-51976052 chr3:51975996-51976010
22	HCFC1	chr3:51975763-51976705	K562	blood:	n/a	n/a
23	POLR2A	chr3:51976034-51976497	K562	blood:	n/a	n/a
24	ZNF263	chr3:51975715-51976838	HEK293-T-REx	kidney:	n/a	chr3:51976283-51976292
25	CTCF	chr3:51976160-51976310	HEEpiC	esophagus:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
26	BRCA1	chr3:51975723-51976613	GM12878	blood:	n/a	n/a
27	YY1	chr3:51975676-51976464	GM12891	blood:	n/a	chr3:51976233-51976244 chr3:51975944-51975955
28	POLR2A	chr3:51975531-51977401	GM12892	blood:	n/a	n/a
29	ELF1	chr3:51975887-51976354	K562	blood:	n/a	chr3:51975993-51976005 chr3:51976142-51976155 chr3:51976143-51976152 chr3:51975903-51975915
30	MAZ	chr3:51975673-51977373	HepG2	liver:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
31	POLR2A	chr3:51975668-51977272	MCF10A-Er-Src	breast:	n/a	n/a
32	CTCF	chr3:51976080-51976413	MCF-7	breast:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
33	POLR2A	chr3:51975649-51976642	HL-60	blood:	n/a	n/a
34	TEAD4	chr3:51976087-51976498	H1-hESC	embryonic stem cell:	n/a	n/a
35	USF1	chr3:51975785-51976502	SK-N-SH_RA	brain:	n/a	n/a
36	CTCF	chr3:51976134-51976399	ECC-1	luminal epithelium:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
37	GABPA	chr3:51975801-51976495	HepG2	liver:	n/a	chr3:51976163-51976177
38	CTCF	chr3:51976160-51976310	K562	blood:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
39	POU2F2	chr3:51976151-51976433	GM12878	blood:	n/a	n/a
40	CTCF	chr3:51975886-51976407	Kidney_OC	kidney:	n/a	chr3:51976231-51976249 chr3:51976002-51976015 chr3:51975889-51975898 chr3:51976234-51976247 chr3:51976232-51976248
41	CTCF	chr3:51976075-51976426	GM19240	blood:	n/a	chr3:51976231-51976249 chr3:51976234-51976247 chr3:51976232-51976248
42	BRCA1	chr3:51976173-51976537	HepG2	liver:	n/a	n/a
43	MAX	chr3:51975542-51976773	ECC-1	luminal epithelium:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
44	TBP	chr3:51975827-51976574	GM12878	blood:	n/a	n/a
45	JUND	chr3:51975797-51976618	K562	blood:	n/a	n/a
46	MYBL2	chr3:51975749-51976866	HepG2	liver:	n/a	n/a
47	EP300	chr3:51975844-51976683	HepG2	liver:	n/a	n/a
48	MAX	chr3:51975393-51977389	Hela-S3	cervix:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
49	UBTF	chr3:51975981-51976538	K562	blood:	n/a	n/a
50	TAF1	chr3:51975711-51976522	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:51976245-51976295	MCF-7	breast:	n/a
2	chr3:51976245-51976295	NHBE	bronchial:	n/a
3	chr3:51976254-51976304	NT2-D1	testis:	n/a
4	chr3:51976245-51976295	HRPEpiC	eye:	n/a
5	chr3:51976245-51976295	PANC-1	pancreas:	n/a
6	chr3:51976254-51976304	HPAEpiC	pulmonary alveolar:	n/a
7	chr3:51976245-51976295	ECC-1	luminal epithelium:	n/a
8	chr3:51976254-51976304	NHBE	bronchial:	n/a
9	chr3:51976254-51976304	U87	brain:	n/a
10	chr3:51976254-51976304	AG04449	skin:	fetal
11	chr3:51976254-51976304	IMR90	lung:	fetal
12	chr3:51976245-51976295	MCF10A-Er-Src	breast:	n/a
13	chr3:51976245-51976295	A549	lung:	n/a
14	chr3:51976245-51976295	NHDF-neo	bronchial:	n/a
15	chr3:51976245-51976295	HCT-116	colon:	n/a
16	chr3:51976245-51976295	AoSMC	blood vessel:	n/a
17	chr3:51976245-51976295	HCM	heart:	n/a
18	chr3:51976254-51976304	HRE	kidney:	n/a
19	chr3:51976245-51976295	U87	brain:	n/a
20	chr3:51976254-51976304	SK-N-SH_RA	brain:	n/a
21	chr3:51976254-51976304	GM12891	blood:	n/a
22	chr3:51976254-51976304	SAEC	small airway:	n/a
23	chr3:51976245-51976295	GM12878	blood:	n/a
24	chr3:51976254-51976304	Caco-2	colon:	n/a
25	chr3:51976254-51976304	A549	lung:	n/a
26	chr3:51976254-51976304	RPTEC	kidney:	n/a
27	chr3:51976254-51976304	HepG2	liver:	n/a
28	chr3:51976254-51976304	AG09309	skin:	n/a
29	chr3:51976254-51976304	GM06990	blood:	n/a
30	chr3:51976254-51976304	Hela-S3	cervix:	n/a
31	chr3:51976254-51976304	AoSMC	blood vessel:	n/a
32	chr3:51976245-51976295	Caco-2	colon:	n/a
33	chr3:51976245-51976295	HUVEC	blood vessel:	n/a
34	chr3:51976245-51976295	BJ	skin:	n/a
35	chr3:51976254-51976304	GM12892	blood:	n/a
36	chr3:51976254-51976304	PFSK-1	brain:	n/a
37	chr3:51976254-51976304	HIPEpiC	eye:	n/a
38	chr3:51976245-51976295	H1-hESC	embryonic stem cell:	embryo
39	chr3:51976245-51976295	HRE	kidney:	n/a
40	chr3:51976245-51976295	T-47D	breast:	n/a
41	chr3:51976245-51976295	AG09309	skin:	n/a
42	chr3:51976254-51976304	SK-N-MC	brain:	n/a
43	chr3:51976245-51976295	ProgFib	skin:	n/a
44	chr3:51976254-51976304	HNPCEpiC	eye:	n/a
45	chr3:51976245-51976295	HEEpiC	esophagus:	n/a
46	chr3:51976245-51976295	BE2_C	brain:	n/a
47	chr3:51976254-51976304	AG09319	gingival:	n/a
48	chr3:51976254-51976304	HL-60	blood:	n/a
49	chr3:51976245-51976295	HEK293	kidney:	embryo
50	chr3:51976245-51976295	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51975872..51976824-chr3:52007664..52008404,2	Hela-S3	cervix:
2	chr2:207024299..207025136-chr3:51976237..51976774,2	Hela-S3	cervix:
3	chr3:51975062..51978431-chr3:52015984..52020263,5	K562	blood:
4	chr3:51975614..51976314-chr5:43120889..43121451,2	Hela-S3	cervix:
5	chr3:51974812..51978768-chr3:52006594..52010604,6	MCF-7	breast:
6	chr3:51974147..51980389-chr3:52024451..52030996,12	K562	blood:
7	chr3:51974226..51977659-chr3:52020694..52024166,4	K562	blood:
8	chr3:51974734..51977966-chr3:52006518..52010028,6	MCF-7	breast:
9	chr3:51975804..51978871-chr3:52028445..52030301,4	K562	blood:
10	chr16:30076382..30077075-chr3:51975737..51976462,2	Hela-S3	cervix:
11	chr3:51974644..51978429-chr3:52029121..52032128,7	MCF-7	breast:
12	chr3:51862209..51864973-chr3:51975409..51978321,2	MCF-7	breast:
13	chr3:51975879..51978347-chr3:52015319..52018171,3	MCF-7	breast:
14	chr17:62502225..62502846-chr3:51975879..51976759,2	Hela-S3	cervix:
15	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
16	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
17	chr3:51974725..51977771-chr3:52005335..52009465,8	K562	blood:
18	chr3:51976078..51979243-chr3:51993727..51997610,4	K562	blood:
19	chr3:51975816..51976930-chr3:52016726..52017409,3	Hela-S3	cervix:
20	chr13:111365185..111365797-chr3:51976007..51976697,2	Hela-S3	cervix:
21	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
22	chr3:51976262..51976887-chr6:89790047..89790875,2	NB4	blood:
23	chr3:51974263..51977386-chr3:52088681..52091436,3	K562	blood:
24	chr3:51974392..51977854-chr3:52027120..52030701,3	MCF-7	breast:
25	chr3:51975763..51976713-chr3:52007592..52008460,5	K562	blood:
26	chr3:51739711..51741988-chr3:51976226..51978640,2	K562	blood:
27	chr1:45186750..45187594-chr3:51975747..51976594,2	HCT-116	colon:
28	chr3:51974179..51978718-chr3:52004198..52010829,11	K562	blood:
29	chr3:51975782..51976919-chr3:52007634..52008466,4	MCF-7	breast:
30	chr3:51974624..51978885-chr3:52015984..52028227,23	K562	blood:
31	chr3:51975678..51978117-chr3:52018353..52021936,3	MCF-7	breast:
32	chr3:51975795..51976454-chr3:52007861..52008453,3	MCF-7	breast:

Variant related genes	Relation type
PARP3	TF binding region
RRP9	TF binding region
RRP9	CpG island
PARP3	CpG island
ENSG00000248487	Chromatin interaction
ENSG00000114942	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000229972	Chromatin interaction
ENSG00000149925	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000164082	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000164086	Chromatin interaction
ENSG00000146278	Chromatin interaction
ENSG00000271931	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000272762	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000090097	Chromatin interaction
ENSG00000023228	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs178918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323869	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323872	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323878	1.00[AMR][1000 genomes]
rs323880	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323889	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323891	1.00[AMR][1000 genomes]
rs323896	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323900	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs422304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56746340	1.00[AMR][1000 genomes]
rs57384151	1.00[AMR][1000 genomes]
rs6446141	1.00[AMR][1000 genomes]
rs72961930	1.00[AMR][1000 genomes]
rs72961999	1.00[AMR][1000 genomes]
rs72964016	1.00[AMR][1000 genomes]
rs7426999	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7636204	1.00[AMR][1000 genomes]
rs9683234	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv590280	chr3:51967439-51978327	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
8	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51974400-51976400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:51974400-51976400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr3:51974400-51976400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:51974400-51976400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr3:51974600-51976600	Active TSS	A549	lung
6	chr3:51974600-51976800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:51974800-51976600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:51974800-51976600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:51974800-51976600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:51975000-51976400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:51975000-51976400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:51975000-51976400	Active TSS	GM12878-XiMat	blood
13	chr3:51975000-51976400	Active TSS	NHDF-Ad	bronchial
14	chr3:51975000-51976600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:51975000-51976600	Active TSS	Lung	lung
16	chr3:51975000-51976800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr3:51975000-51976800	Active TSS	Small Intestine	intestine
18	chr3:51975200-51976400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:51975200-51976400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:51975200-51976400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:51975200-51976400	Active TSS	Fetal Intestine Large	intestine
22	chr3:51975200-51976400	Active TSS	K562	blood
23	chr3:51975200-51976600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr3:51975200-51976600	Active TSS	Ovary	ovary
25	chr3:51975200-51977400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr3:51975400-51976400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr3:51975400-51976400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:51975400-51976400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:51975400-51976400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:51975400-51976400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr3:51975400-51976400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:51975400-51976400	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr3:51975400-51976400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:51975400-51976400	Active TSS	Muscle Satellite Cultured Cells	--
35	chr3:51975400-51976400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:51975400-51976400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:51975400-51976400	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr3:51975400-51976400	Active TSS	Fetal Intestine Small	intestine
39	chr3:51975400-51976400	Active TSS	Fetal Kidney	kidney
40	chr3:51975400-51976400	Active TSS	Fetal Lung	lung
41	chr3:51975400-51976400	Active TSS	Fetal Stomach	stomach
42	chr3:51975400-51976400	Active TSS	Rectal Smooth Muscle	rectum
43	chr3:51975400-51976400	Active TSS	Right Ventricle	heart
44	chr3:51975400-51976400	Active TSS	Dnd41	blood
45	chr3:51975400-51976400	Active TSS	Hela-S3	cervix
46	chr3:51975400-51976400	Active TSS	HSMM	muscle
47	chr3:51975400-51976400	Active TSS	HSMMtube	muscle
48	chr3:51975400-51976400	Active TSS	NHEK	skin
49	chr3:51975400-51976600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:51975400-51976600	Active TSS	Esophagus	oesophagus

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