Variant report

Variant	rs73012149
Chromosome Location	chr3:156877299-156877300
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	YY1	chr3:156877183-156877400	HCT-116	colon:	n/a	chr3:156877370-156877379 chr3:156877323-156877332 chr3:156877327-156877349 chr3:156877318-156877332 chr3:156877327-156877337 chr3:156877367-156877376 chr3:156877315-156877329 chr3:156877365-156877379 chr3:156877330-156877338 chr3:156877370-156877381 chr3:156877367-156877378 chr3:156877327-156877337
2	POLR2A	chr3:156876714-156879143	HUVEC	blood vessel:	n/a	n/a
3	ZNF384	chr3:156877122-156877403	K562	blood:	n/a	n/a
4	POLR2A	chr3:156875169-156879293	MCF10A-Er-Src	breast:	n/a	n/a
5	TCF12	chr3:156876865-156878956	A549	lung:	n/a	n/a
6	POLR2A	chr3:156876034-156879187	GM12892	blood:	n/a	n/a
7	CTCF	chr3:156877160-156877310	GM12868	blood:	n/a	n/a
8	POLR2A	chr3:156877214-156877704	A549	lung:	n/a	n/a
9	TBP	chr3:156877008-156879123	H1-hESC	embryonic stem cell:	n/a	chr3:156878569-156878580
10	MTA3	chr3:156876897-156879216	GM12878	blood:	n/a	n/a
11	TAF1	chr3:156877022-156878719	SK-N-SH	brain:	n/a	n/a
12	YY1	chr3:156876982-156878314	ECC-1	luminal epithelium:	n/a	chr3:156877370-156877379 chr3:156877323-156877332 chr3:156878064-156878073 chr3:156877327-156877349 chr3:156878059-156878073 chr3:156877318-156877332 chr3:156878065-156878079 chr3:156877327-156877337 chr3:156877367-156877376 chr3:156877315-156877329 chr3:156877365-156877379 chr3:156877330-156877338 chr3:156877370-156877381 chr3:156877367-156877378 chr3:156877327-156877337
13	STAT3	chr3:156876918-156877302	MCF10A-Er-Src	breast:	n/a	chr3:156877105-156877116
14	YY1	chr3:156876764-156878590	SK-N-SH	brain:	n/a	chr3:156877370-156877379 chr3:156877323-156877332 chr3:156878064-156878073 chr3:156877327-156877349 chr3:156878059-156878073 chr3:156877318-156877332 chr3:156878065-156878079 chr3:156877327-156877337 chr3:156877367-156877376 chr3:156877315-156877329 chr3:156877365-156877379 chr3:156877330-156877338 chr3:156877370-156877381 chr3:156877367-156877378 chr3:156877327-156877337
15	POLR2A	chr3:156877099-156878944	GM18526	blood:	n/a	n/a
16	MAZ	chr3:156877219-156877325	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:156876999-156877301	SK-N-SH	brain:	n/a	n/a
18	TAF1	chr3:156877147-156877399	GM12892	blood:	n/a	n/a
19	CTCF	chr3:156877216-156877351	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:156877208-156877342	MCF-7	breast:	n/a	n/a
21	POLR2A	chr3:156877184-156878926	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:156876806-156878978	GM12891	blood:	n/a	n/a
23	TAF1	chr3:156876999-156877431	Hela-S3	cervix:	n/a	n/a
24	TCF7L2	chr3:156877225-156878701	HCT-116	colon:	n/a	chr3:156878378-156878388
25	POU2F2	chr3:156877004-156877417	GM12878	blood:	n/a	chr3:156877372-156877384
26	POLR2A	chr3:156876935-156878776	GM12878	blood:	n/a	n/a
27	ATF2	chr3:156876895-156877430	GM12878	blood:	n/a	n/a
28	CTCF	chr3:156877200-156877350	BJ	skin:	n/a	n/a
29	TAF1	chr3:156877145-156877411	GM12891	blood:	n/a	n/a
30	TAF1	chr3:156877047-156878529	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:156876253-156879191	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:156876812-156879195	GM12892	blood:	n/a	n/a
33	POLR2A	chr3:156875365-156879216	IMR90	lung:	n/a	n/a
34	POLR2A	chr3:156875302-156879130	H1-hESC	embryonic stem cell:	n/a	n/a
35	RCOR1	chr3:156877189-156877432	K562	blood:	n/a	n/a
36	CTCF	chr3:156877160-156877310	RPTEC	kidney:	n/a	n/a
37	USF2	chr3:156876888-156878719	GM12878	blood:	n/a	chr3:156877313-156877329 chr3:156877367-156877383 chr3:156877369-156877385
38	SPI1	chr3:156876942-156877412	GM12891	blood:	n/a	chr3:156877349-156877362
39	CTCF	chr3:156877180-156877330	HA-sp	spinal cord:	n/a	n/a
40	POLR2A	chr3:156874371-156879129	GM12891	blood:	n/a	n/a
41	POLR2A	chr3:156876914-156878985	U87	brain:	n/a	n/a
42	POLR2A	chr3:156873921-156879347	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr3:156876544-156877362	GM12892	blood:	n/a	n/a
44	ETS1	chr3:156877147-156877610	K562	blood:	n/a	chr3:156877287-156877294 chr3:156877367-156877378 chr3:156877370-156877381
45	YY1	chr3:156876987-156878738	A549	lung:	n/a	chr3:156877370-156877379 chr3:156877323-156877332 chr3:156878064-156878073 chr3:156877327-156877349 chr3:156878059-156878073 chr3:156877318-156877332 chr3:156878065-156878079 chr3:156877327-156877337 chr3:156877367-156877376 chr3:156877315-156877329 chr3:156877365-156877379 chr3:156877330-156877338 chr3:156877370-156877381 chr3:156877367-156877378 chr3:156877327-156877337
46	POLR2A	chr3:156877186-156878637	A549	lung:	n/a	n/a
47	RUNX3	chr3:156876837-156877520	GM12878	blood:	n/a	n/a
48	JUND	chr3:156877190-156877409	K562	blood:	n/a	n/a
49	CTCF	chr3:156877240-156877390	GM12865	blood:	n/a	n/a
50	GABPA	chr3:156877088-156877391	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:156877271..156878729-chr3:156891908..156893288,13	MCF-7	breast:
2	chr3:156270417..156272669-chr3:156876892..156879496,3	MCF-7	breast:
3	chr3:156806442..156808690-chr3:156876399..156878751,3	K562	blood:
4	chr3:156533151..156536166-chr3:156876536..156878958,4	MCF-7	breast:
5	chr3:156876906..156878652-chr5:112849281..112850980,2	MCF-7	breast:
6	chr3:156271311..156273163-chr3:156875258..156877901,2	MCF-7	breast:
7	chr3:156533566..156537799-chr3:156875553..156879495,5	MCF-7	breast:
8	chr3:156270403..156273229-chr3:156876136..156878579,3	K562	blood:
9	chr3:156877079..156878844-chr3:156892396..156893424,14	MCF-7	breast:
10	chr3:156391251..156395598-chr3:156875832..156879722,8	K562	blood:
11	chr3:156542707..156546513-chr3:156875626..156880471,4	K562	blood:
12	chr19:14116306..14117077-chr3:156877017..156877934,2	Hela-S3	cervix:
13	chr3:156390449..156395705-chr3:156876136..156879645,10	MCF-7	breast:
14	chr3:156876658..156879378-chr3:156891661..156893506,34	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000241770	TF binding region
CCNL1	TF binding region
ENSG00000240875	Chromatin interaction
ENSG00000047188	Chromatin interaction
ENSG00000222675	Chromatin interaction
ENSG00000241135	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000132005	Chromatin interaction
ENSG00000243176	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000114850	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs58032323	1.00[AMR][1000 genomes]
rs59496343	1.00[AFR][1000 genomes]
rs61553506	0.89[AFR][1000 genomes]
rs73012142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73012145	1.00[AMR][1000 genomes]
rs73012147	1.00[AMR][1000 genomes]
rs73012153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73012159	0.82[AFR][1000 genomes]
rs73012167	0.89[AFR][1000 genomes]
rs73012171	0.89[AFR][1000 genomes]
rs73012173	0.87[AFR][1000 genomes]
rs73012176	0.89[AFR][1000 genomes]
rs73012181	0.89[AFR][1000 genomes]
rs73012196	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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
3	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription 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 miRNA target site	139 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	chr3:156871800-156879200	Active TSS	Right Ventricle	heart
2	chr3:156872000-156877800	Active TSS	Right Atrium	heart
3	chr3:156872000-156878600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:156872200-156879000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
5	chr3:156872400-156879200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:156872600-156877800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
7	chr3:156873800-156877800	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:156874200-156877800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
9	chr3:156874800-156879000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:156875000-156879000	Active TSS	Psoas Muscle	Psoas
11	chr3:156875400-156878800	Active TSS	Ovary	ovary
12	chr3:156875800-156879000	Active TSS	Left Ventricle	heart
13	chr3:156876000-156877800	Active TSS	Aorta	Aorta
14	chr3:156876000-156878400	Active TSS	Fetal Brain Female	brain
15	chr3:156876000-156878800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:156876200-156879000	Active TSS	Small Intestine	intestine
17	chr3:156876400-156878800	Active TSS	Fetal Intestine Small	intestine
18	chr3:156876400-156878800	Active TSS	Stomach Mucosa	stomach
19	chr3:156876400-156879000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:156876600-156877400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:156876600-156877400	Active TSS	Brain Germinal Matrix	brain
22	chr3:156876600-156878000	Active TSS	Colonic Mucosa	Colon
23	chr3:156876600-156878600	Active TSS	Lung	lung
24	chr3:156876600-156878600	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr3:156876600-156878800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:156876600-156878800	Bivalent/Poised TSS	HepG2	liver
27	chr3:156876600-156879000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr3:156876600-156879000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:156876600-156879000	Active TSS	Fetal Brain Male	brain
30	chr3:156876600-156879200	Active TSS	Fetal Muscle Trunk	muscle
31	chr3:156876800-156878200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:156876800-156878200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr3:156876800-156878200	Active TSS	HUVEC	blood vessel
34	chr3:156876800-156878400	Active TSS	Fetal Thymus	thymus
35	chr3:156876800-156878600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:156876800-156878600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:156876800-156878600	Active TSS	Adipose Nuclei	Adipose
38	chr3:156876800-156878600	Active TSS	Fetal Muscle Leg	muscle
39	chr3:156876800-156878800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:156876800-156878800	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr3:156876800-156878800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:156876800-156878800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:156876800-156878800	Active TSS	Brain Angular Gyrus	brain
44	chr3:156876800-156878800	Active TSS	Brain Hippocampus Middle	brain
45	chr3:156876800-156878800	Active TSS	Fetal Intestine Large	intestine
46	chr3:156876800-156878800	Active TSS	Fetal Stomach	stomach
47	chr3:156876800-156878800	Active TSS	Stomach Smooth Muscle	stomach
48	chr3:156876800-156878800	Active TSS	Thymus	Thymus
49	chr3:156876800-156878800	Active TSS	NHLF	lung
50	chr3:156876800-156879000	Active TSS	H9 Cell Line	embryonic stem cell

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