Variant report

Variant	rs6749343
Chromosome Location	chr2:38830412-38830413
allele	A/G
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	POLR2A	chr2:38830240-38830467	A549	lung:	n/a	n/a
2	POLR2A	chr2:38828488-38830465	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr2:38830381-38830484	GM20000	blood:	n/a	n/a
4	GABPA	chr2:38829345-38830587	MCF-7	breast:	n/a	n/a
5	POLR2A	chr2:38829453-38830716	PFSK-1	brain:	n/a	n/a
6	GABPA	chr2:38829542-38830511	MCF-7	breast:	n/a	n/a
7	STAT5A	chr2:38829889-38830960	GM12878	blood:	n/a	chr2:38830200-38830212
8	IRF3	chr2:38830093-38830516	HepG2	liver:	n/a	chr2:38830259-38830268
9	YY1	chr2:38830024-38830497	GM12891	blood:	n/a	chr2:38830141-38830150
10	SIN3AK20	chr2:38829163-38830978	SK-N-SH	brain:	n/a	n/a
11	EP300	chr2:38829751-38830934	HepG2	liver:	n/a	chr2:38830177-38830193 chr2:38829849-38829858 chr2:38829773-38829789
12	TEAD4	chr2:38829813-38830976	K562	blood:	n/a	n/a
13	RAD21	chr2:38830383-38831116	A549	lung:	n/a	n/a
14	UBTF	chr2:38828546-38830909	K562	blood:	n/a	n/a
15	MAX	chr2:38829019-38831087	HepG2	liver:	n/a	n/a
16	STAT5A	chr2:38829855-38830979	K562	blood:	n/a	chr2:38830200-38830212
17	CTCF	chr2:38830340-38830490	WERI-Rb-1	eye:	n/a	n/a
18	E2F4	chr2:38829682-38830917	K562	blood:	n/a	chr2:38830234-38830245 chr2:38830233-38830245 chr2:38830237-38830244 chr2:38830237-38830244 chr2:38830237-38830244
19	RCOR1	chr2:38828426-38831063	IMR90	lung:	n/a	n/a
20	TBL1XR1	chr2:38829856-38830998	K562	blood:	n/a	n/a
21	FOXA2	chr2:38829840-38830487	A549	lung:	n/a	n/a
22	CTCF	chr2:38830400-38830550	Hela-S3	cervix:	n/a	n/a
23	YY1	chr2:38829344-38830866	GM12878	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
24	SIN3AK20	chr2:38828533-38831144	MCF-7	breast:	n/a	n/a
25	ELF1	chr2:38829855-38830449	MCF-7	breast:	n/a	chr2:38830084-38830097
26	SIN3AK20	chr2:38830028-38830445	SK-N-SH	brain:	n/a	n/a
27	CHD2	chr2:38829207-38830825	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr2:38830320-38830470	GM12870	blood:	n/a	n/a
29	REST	chr2:38829830-38830454	SK-N-SH	brain:	n/a	chr2:38830014-38830027 chr2:38830026-38830039
30	TAF1	chr2:38829302-38830510	K562	blood:	n/a	n/a
31	ZBTB7A	chr2:38828985-38830833	ECC-1	luminal epithelium:	n/a	n/a
32	E2F6	chr2:38829843-38831033	A549	lung:	n/a	chr2:38830233-38830245 chr2:38830237-38830244 chr2:38830237-38830244 chr2:38830237-38830244
33	EGR1	chr2:38829402-38831083	HCT-116	colon:	n/a	chr2:38830139-38830152 chr2:38830140-38830149 chr2:38830134-38830156 chr2:38829801-38829811 chr2:38830139-38830152 chr2:38830138-38830153 chr2:38830139-38830152 chr2:38830138-38830152 chr2:38830139-38830149 chr2:38829798-38829811 chr2:38830140-38830151 chr2:38830139-38830152 chr2:38830136-38830150
34	SIN3AK20	chr2:38829621-38830884	K562	blood:	n/a	n/a
35	MYC	chr2:38829997-38830837	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr2:38828985-38830918	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr2:38829624-38830685	U87	brain:	n/a	n/a
38	NFATC1	chr2:38830201-38830956	GM12878	blood:	n/a	n/a
39	HA-E2F1	chr2:38829827-38831039	MCF-7	breast:	n/a	chr2:38830233-38830245 chr2:38830237-38830244 chr2:38830237-38830244 chr2:38830237-38830244
40	MAX	chr2:38829399-38831046	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr2:38829066-38830968	H1-neurons	neurons:	n/a	n/a
42	PAX5	chr2:38829705-38830499	GM12892	blood:	n/a	n/a
43	CREB1	chr2:38829835-38831040	H1-hESC	embryonic stem cell:	n/a	n/a
44	FOSL2	chr2:38829811-38831045	A549	lung:	n/a	chr2:38830257-38830266
45	POLR2A	chr2:38829728-38830514	GM12891	blood:	n/a	n/a
46	POLR2A	chr2:38829845-38830522	GM12878	blood:	n/a	n/a
47	SPI1	chr2:38830093-38830470	HL-60	blood:	n/a	n/a
48	REST	chr2:38829723-38830949	HepG2	liver:	n/a	chr2:38830014-38830027 chr2:38830026-38830039 chr2:38829806-38829819
49	POLR2A	chr2:38829773-38830506	GM18951	blood:	n/a	n/a
50	CTCF	chr2:38830372-38830505	Kidney_OC	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38828577..38831705-chr2:38976861..38979916,6	MCF-7	breast:
2	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
3	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
4	chr2:38829797..38830463-chr9:77643062..77643621,2	HCT-116	colon:
5	chr2:38823060..38827854-chr2:38827983..38831423,11	MCF-7	breast:
6	chr2:38829777..38830414-chr5:33440760..33441422,2	Hela-S3	cervix:
7	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
8	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
9	chr2:38816751..38822030-chr2:38827238..38830922,5	MCF-7	breast:
10	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
11	chr2:38829496..38831232-chr2:38893143..38894875,2	MCF-7	breast:

Variant related genes	Relation type
HNRNPLL	TF binding region
ENSG00000143891	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000156017	Chromatin interaction
ENSG00000232518	Chromatin interaction
ENSG00000113407	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10204680	0.83[ASN][1000 genomes]
rs10495880	0.90[EUR][1000 genomes]
rs12987111	0.89[EUR][1000 genomes]
rs12990659	0.89[EUR][1000 genomes]
rs12991911	0.88[EUR][1000 genomes]
rs12992482	0.98[ASN][1000 genomes]
rs12995222	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12996029	0.90[EUR][1000 genomes]
rs13010091	0.98[ASN][1000 genomes]
rs13011896	0.95[ASN][1000 genomes]
rs13015860	0.98[ASN][1000 genomes]
rs13016108	0.98[ASN][1000 genomes]
rs13016885	0.86[ASN][1000 genomes]
rs13025153	0.95[ASN][1000 genomes]
rs13415823	0.92[ASN][1000 genomes]
rs13431551	0.85[EUR][1000 genomes]
rs1368114	0.85[EUR][1000 genomes]
rs1540436	0.88[EUR][1000 genomes]
rs17022983	0.98[ASN][1000 genomes]
rs17421743	0.94[EUR][1000 genomes]
rs17493573	0.89[EUR][1000 genomes]
rs17493692	0.98[ASN][1000 genomes]
rs17575960	0.81[EUR][1000 genomes]
rs1864829	0.91[EUR][1000 genomes]
rs1864830	0.94[EUR][1000 genomes]
rs2116383	0.86[ASN][1000 genomes]
rs2116385	0.86[ASN][1000 genomes]
rs2163551	0.95[ASN][1000 genomes]
rs2253519	0.84[EUR][1000 genomes]
rs2373420	0.88[ASN][1000 genomes]
rs2373422	0.98[ASN][1000 genomes]
rs34145681	0.83[ASN][1000 genomes]
rs34462852	0.90[EUR][1000 genomes]
rs34533895	0.94[EUR][1000 genomes]
rs35219064	0.89[EUR][1000 genomes]
rs35273515	0.84[ASN][1000 genomes]
rs35492507	0.86[EUR][1000 genomes]
rs35613649	0.86[ASN][1000 genomes]
rs35679136	0.83[EUR][1000 genomes]
rs35734673	0.90[EUR][1000 genomes]
rs35861429	0.95[ASN][1000 genomes]
rs4268910	0.89[EUR][1000 genomes]
rs6544169	0.84[EUR][1000 genomes]
rs6710118	0.84[EUR][1000 genomes]
rs67326552	0.93[ASN][1000 genomes]
rs6736320	0.84[EUR][1000 genomes]
rs6742843	0.86[ASN][1000 genomes]
rs67772386	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs72907903	0.90[EUR][1000 genomes]
rs72909831	0.83[ASN][1000 genomes]
rs7583318	0.85[ASN][1000 genomes]
rs7609065	0.82[EUR][1000 genomes]
rs919698	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38825000-38830600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:38825200-38831000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:38825600-38830800	Active TSS	Stomach Smooth Muscle	stomach
4	chr2:38826200-38830800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:38826400-38830600	Active TSS	K562	blood
6	chr2:38826400-38831400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:38826800-38830600	Active TSS	NHLF	lung
8	chr2:38826800-38831000	Active TSS	Duodenum Mucosa	Duodenum
9	chr2:38827000-38830600	Active TSS	Aorta	Aorta
10	chr2:38827000-38830800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:38827000-38830800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:38827000-38830800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:38827000-38830800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:38827000-38831400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr2:38827200-38830600	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr2:38827200-38830600	Active TSS	NH-A	brain
17	chr2:38827200-38830800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:38827200-38830800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr2:38827200-38830800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:38827200-38830800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:38827200-38830800	Active TSS	Fetal Intestine Small	intestine
22	chr2:38827200-38831000	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr2:38827200-38831000	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr2:38827200-38831000	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr2:38827200-38831200	Active TSS	Brain Germinal Matrix	brain
26	chr2:38827400-38830600	Active TSS	Fetal Stomach	stomach
27	chr2:38827400-38830800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr2:38827400-38830800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr2:38827400-38830800	Bivalent/Poised TSS	HepG2	liver
30	chr2:38827400-38831000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr2:38827400-38831000	Active TSS	Right Ventricle	heart
32	chr2:38827400-38831200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:38827600-38830600	Active TSS	Colon Smooth Muscle	Colon
34	chr2:38827600-38830800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:38827600-38830800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr2:38827600-38830800	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr2:38827600-38830800	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr2:38827600-38830800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:38827600-38830800	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr2:38827600-38830800	Active TSS	Brain Angular Gyrus	brain
41	chr2:38827600-38830800	Active TSS	HSMM	muscle
42	chr2:38827600-38831000	Active TSS	Brain Anterior Caudate	brain
43	chr2:38827600-38831000	Active TSS	Thymus	Thymus
44	chr2:38827600-38831400	Active TSS	Colonic Mucosa	Colon
45	chr2:38827800-38830600	Active TSS	Hela-S3	cervix
46	chr2:38827800-38830800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:38827800-38830800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr2:38827800-38830800	Active TSS	Esophagus	oesophagus
49	chr2:38827800-38830800	Active TSS	Fetal Intestine Large	intestine
50	chr2:38827800-38831000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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