Variant report

Variant	rs3759402
Chromosome Location	chr12:121021193-121021194
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	JUND	chr12:121021178-121021793	K562	blood:	n/a	n/a
2	RAD21	chr12:121021069-121021702	MCF-7	breast:	n/a	chr12:121021368-121021387
3	RAD21	chr12:121021187-121021618	H1-hESC	embryonic stem cell:	n/a	chr12:121021368-121021387
4	SMC3	chr12:121021024-121021968	SK-N-SH	brain:	n/a	n/a
5	SMC3	chr12:121021135-121021699	HepG2	liver:	n/a	n/a
6	RAD21	chr12:121021027-121021789	ECC-1	luminal epithelium:	n/a	chr12:121021368-121021387
7	YY1	chr12:121021189-121021749	GM12878	blood:	n/a	n/a
8	BACH1	chr12:121021129-121021504	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAZ	chr12:121021172-121021597	GM12878	blood:	n/a	n/a
10	RAD21	chr12:121020989-121021985	HCT-116	colon:	n/a	chr12:121021368-121021387
11	CTCF	chr12:121021177-121021556	T-47D	breast:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
12	RAD21	chr12:121021189-121021533	SK-N-SH_RA	brain:	n/a	chr12:121021368-121021387
13	MAX	chr12:121021059-121021956	A549	lung:	n/a	n/a
14	RAD21	chr12:121021165-121021800	Hela-S3	cervix:	n/a	chr12:121021368-121021387
15	RAD21	chr12:121021191-121021581	GM12878	blood:	n/a	chr12:121021368-121021387
16	CTCF	chr12:121021138-121021634	H1-hESC	embryonic stem cell:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
17	CTCF	chr12:121021160-121021310	A549	lung:	n/a	n/a
18	CTCF	chr12:121021059-121021715	MCF-7	breast:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
19	CTCF	chr12:121021173-121021467	A549	lung:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
20	SIN3A	chr12:121021167-121021796	H1-hESC	embryonic stem cell:	n/a	n/a
21	ATF2	chr12:121021125-121021525	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr12:121021091-121021605	ECC-1	luminal epithelium:	n/a	chr12:121021368-121021387
23	CTCF	chr12:121020877-121021911	HCT-116	colon:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
24	POLR2A	chr12:121021177-121021231	HUVEC	blood vessel:	n/a	n/a
25	CBX3	chr12:121021128-121021937	K562	blood:	n/a	chr12:121021332-121021343
26	RAD21	chr12:121021088-121021738	A549	lung:	n/a	chr12:121021368-121021387
27	CTCF	chr12:121021157-121021556	A549	lung:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
28	RAD21	chr12:121021188-121021624	A549	lung:	n/a	chr12:121021368-121021387
29	CTCF	chr12:121021100-121021618	HepG2	liver:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
30	CTCF	chr12:121021078-121021732	HCT-116	colon:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
31	RAD21	chr12:121021084-121021800	MCF-7	breast:	n/a	chr12:121021368-121021387
32	RAD21	chr12:121021096-121021689	HepG2	liver:	n/a	chr12:121021368-121021387
33	SMC3	chr12:121021165-121021631	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr12:121021162-121021598	GM12878	blood:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
35	CTCF	chr12:121021164-121021572	K562	blood:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
36	CTCF	chr12:121021104-121021605	K562	blood:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
37	CTCF	chr12:121021182-121021514	SK-N-SH_RA	brain:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
38	ATF2	chr12:121021128-121021571	H1-hESC	embryonic stem cell:	n/a	n/a
39	SMC3	chr12:121021191-121021579	GM12878	blood:	n/a	n/a
40	RAD21	chr12:121020950-121021881	A549	lung:	n/a	chr12:121021368-121021387
41	CTCF	chr12:121021149-121021555	H1-hESC	embryonic stem cell:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
42	CTCF	chr12:121020914-121022043	SK-N-SH	brain:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
43	RAD21	chr12:121020884-121021974	SK-N-SH	brain:	n/a	chr12:121021368-121021387
44	SMC3	chr12:121021171-121021588	K562	blood:	n/a	n/a
45	RAD21	chr12:121021158-121021591	GM12878	blood:	n/a	chr12:121021368-121021387
46	JUND	chr12:121021070-121021791	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr12:121021106-121021655	H1-hESC	embryonic stem cell:	n/a	chr12:121021368-121021387
48	RAD21	chr12:121021169-121021537	GM12878	blood:	n/a	chr12:121021368-121021387
49	CTCF	chr12:121021119-121021579	T-47D	breast:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
50	RAD21	chr12:121021015-121021912	HCT-116	colon:	n/a	chr12:121021368-121021387

No.	Distal block	Cell Line	Cell type
1	chr12:121018631..121021385-chr12:121124185..121125689,2	MCF-7	breast:
2	chr12:121021041..121021897-chr12:121661173..121662030,2	MCF-7	breast:
3	chr12:121020996..121021955-chr12:121087894..121088614,2	K562	blood:
4	chr12:121017632..121023235-chr12:121123750..121127979,5	K562	blood:
5	chr12:120728472..120731126-chr12:121019042..121021642,2	K562	blood:
6	chr12:121021176..121021954-chr12:121086681..121088032,8	MCF-7	breast:
7	chr12:121020078..121022631-chr12:121125640..121127142,2	K562	blood:
8	chr12:121020907..121021484-chr12:121077869..121078415,2	MCF-7	breast:
9	chr12:121021138..121021783-chr12:121084881..121085562,2	K562	blood:
10	chr12:121020899..121021841-chr12:121409286..121409915,3	K562	blood:
11	chr12:121020419..121023213-chr12:121085697..121088719,3	MCF-7	breast:
12	chr12:121020917..121021868-chr12:121533219..121533885,3	K562	blood:
13	chr12:121020875..121021804-chr12:121150905..121152345,4	K562	blood:
14	chr12:121019438..121021278-chr12:121153857..121156212,2	K562	blood:

Variant related genes	Relation type
POP5	TF binding region
ENSG00000256008	Chromatin interaction
ENSG00000157782	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000110917	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11065140	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11065142	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11548262	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11608807	0.90[ASN][1000 genomes]
rs11611781	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611814	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11612519	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11613214	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11614224	0.88[ASN][1000 genomes]
rs11615264	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11615719	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11829765	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16950293	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16950305	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2280168	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35696148	0.83[ASN][1000 genomes]
rs3742049	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3817301	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829291	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4102203	0.84[EUR][1000 genomes]
rs4439575	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57646360	0.83[ASN][1000 genomes]
rs59088579	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59201986	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60162888	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6490292	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66840048	0.95[ASN][1000 genomes]
rs7027	0.90[ASN][1000 genomes]
rs719449	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs719450	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7296473	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7297861	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299954	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314103	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73403923	0.90[ASN][1000 genomes]
rs73403943	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73403947	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73403968	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73403975	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73405628	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7961895	0.90[ASN][1000 genomes]
rs7962410	0.95[ASN][1000 genomes]
rs7964008	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7973555	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv973944	chr12:121017088-121027122	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121019600-121021200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:121019600-121021200	Weak transcription	Spleen	Spleen
3	chr12:121019600-121022000	Weak transcription	Lung	lung
4	chr12:121019600-121027200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:121019800-121021200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:121019800-121021200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:121019800-121021200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:121019800-121021200	Weak transcription	Esophagus	oesophagus
9	chr12:121019800-121021200	Weak transcription	Pancreas	Pancrea
10	chr12:121019800-121021400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:121019800-121021400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:121019800-121021400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:121019800-121021400	Weak transcription	Gastric	stomach
14	chr12:121019800-121021400	Weak transcription	Psoas Muscle	Psoas
15	chr12:121019800-121021400	Weak transcription	Stomach Mucosa	stomach
16	chr12:121019800-121022200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:121019800-121022200	Weak transcription	Aorta	Aorta
18	chr12:121019800-121022200	Weak transcription	Left Ventricle	heart
19	chr12:121019800-121022600	Weak transcription	Small Intestine	intestine
20	chr12:121020000-121021200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:121020000-121021200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:121020000-121021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:121020000-121021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:121020000-121021200	Weak transcription	HSMM	muscle
25	chr12:121020000-121021200	Weak transcription	NH-A	brain
26	chr12:121020000-121021400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:121020000-121021400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:121020000-121021400	Enhancers	Liver	Liver
29	chr12:121020000-121021600	Weak transcription	Right Atrium	heart
30	chr12:121020000-121022200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:121020000-121022200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:121020000-121022200	Weak transcription	Ovary	ovary
33	chr12:121020000-121022200	Weak transcription	Right Ventricle	heart
34	chr12:121020200-121021200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:121020200-121021200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:121020200-121021200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:121020200-121021200	Weak transcription	Colonic Mucosa	Colon
38	chr12:121020200-121021200	Weak transcription	Fetal Thymus	thymus
39	chr12:121020200-121021200	Enhancers	Dnd41	blood
40	chr12:121020200-121021200	Weak transcription	NHDF-Ad	bronchial
41	chr12:121020200-121021200	Weak transcription	NHEK	skin
42	chr12:121020200-121021200	Weak transcription	NHLF	lung
43	chr12:121020200-121021400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:121020400-121021200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:121020600-121021200	Enhancers	Duodenum Mucosa	Duodenum
46	chr12:121020600-121021200	Enhancers	Stomach Smooth Muscle	stomach
47	chr12:121020800-121021200	Enhancers	Primary B cells from cord blood	blood
48	chr12:121020800-121021200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr12:121020800-121021200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:121020800-121021200	Enhancers	Skeletal Muscle Female	skeletal muscle

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