Variant report

Variant	rs3963416
Chromosome Location	chr3:137906485-137906486
allele	C/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	POLR2A	chr3:137905917-137906630	GM10847	blood:	n/a	n/a
2	SIN3A	chr3:137906066-137906566	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:137905839-137907099	GM15510	blood:	n/a	n/a
4	MAX	chr3:137905955-137906885	H1-hESC	embryonic stem cell:	n/a	chr3:137906076-137906086
5	REST	chr3:137905938-137906756	HL-60	blood:	n/a	chr3:137906076-137906089 chr3:137906372-137906382
6	RCOR1	chr3:137905708-137907594	Hela-S3	cervix:	n/a	n/a
7	ZBTB7A	chr3:137906085-137906783	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr3:137906005-137907127	HL-60	blood:	n/a	n/a
9	POLR2A	chr3:137905831-137907118	Raji	blood:	n/a	n/a
10	POLR2A	chr3:137905817-137907325	HUVEC	blood vessel:	n/a	n/a
11	JUND	chr3:137906107-137906577	A549	lung:	n/a	n/a
12	CTCF	chr3:137906440-137906590	BJ	skin:	n/a	n/a
13	SP1	chr3:137905868-137906738	A549	lung:	n/a	chr3:137906075-137906087 chr3:137906076-137906086 chr3:137906076-137906085 chr3:137906075-137906087 chr3:137906077-137906086 chr3:137906076-137906086 chr3:137906076-137906090
14	RUNX3	chr3:137905947-137906583	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:137905700-137907041	GM18505	blood:	n/a	n/a
16	TCF3	chr3:137906174-137906705	GM12878	blood:	n/a	n/a
17	POU2F2	chr3:137906062-137906551	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:137905659-137906687	U87	brain:	n/a	n/a
19	TAF1	chr3:137905963-137907030	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr3:137905920-137907063	HepG2	liver:	n/a	chr3:137906388-137906405 chr3:137906722-137906731 chr3:137906075-137906089 chr3:137906095-137906109 chr3:137906661-137906683
21	POLR2A	chr3:137905711-137907236	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr3:137905971-137906690	PANC-1	pancreas:	n/a	n/a
23	MAX	chr3:137905973-137906620	MCF-7	breast:	n/a	chr3:137906076-137906086
24	POLR2A	chr3:137905620-137907124	GM12891	blood:	n/a	n/a
25	ELF1	chr3:137905918-137906609	MCF-7	breast:	n/a	chr3:137906077-137906089
26	POLR2A	chr3:137905668-137907285	HUVEC	blood vessel:	n/a	n/a
27	TAF1	chr3:137906098-137906570	GM12892	blood:	n/a	n/a
28	POLR2A	chr3:137905895-137906519	HepG2	liver:	n/a	n/a
29	CHD2	chr3:137905952-137906824	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:137905845-137907052	GM18951	blood:	n/a	n/a
31	YY1	chr3:137905878-137907022	H1-hESC	embryonic stem cell:	n/a	chr3:137906388-137906405 chr3:137906722-137906731 chr3:137906075-137906089 chr3:137906095-137906109 chr3:137906661-137906683
32	TAF1	chr3:137905973-137907030	H1-neurons	neurons:	n/a	n/a
33	PBX3	chr3:137905815-137906592	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr3:137906005-137906822	MCF-7	breast:	n/a	n/a
35	RCOR1	chr3:137905651-137906943	HepG2	liver:	n/a	n/a
36	MTA3	chr3:137905778-137907112	GM12878	blood:	n/a	n/a
37	GATA2	chr3:137905681-137907104	SH-SY5Y	brain:	n/a	n/a
38	POLR2A	chr3:137905910-137906984	MCF-7	breast:	n/a	n/a
39	POLR2A	chr3:137905801-137907174	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr3:137905742-137906744	SK-N-SH	brain:	n/a	n/a
41	CHD2	chr3:137905829-137907116	Hela-S3	cervix:	n/a	n/a
42	CEBPB	chr3:137906076-137907416	HepG2	liver:	n/a	n/a
43	MYBL2	chr3:137905985-137906531	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:137905891-137906878	ECC-1	luminal epithelium:	n/a	n/a
45	MAFK	chr3:137905258-137906649	K562	blood:	n/a	n/a
46	POLR2A	chr3:137905834-137906915	HEK293	kidney:	n/a	n/a
47	MAX	chr3:137905828-137907035	GM12878	blood:	n/a	chr3:137906076-137906086
48	POLR2A	chr3:137905809-137906998	GM12878	blood:	n/a	n/a
49	TAF7	chr3:137906063-137906756	H1-hESC	embryonic stem cell:	n/a	n/a
50	FOSL2	chr3:137905954-137906511	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:137904685..137906516-chr3:137939797..137942288,3	K562	blood:
2	chr3:137904820..137906747-chr3:137954562..137956605,2	K562	blood:
3	chr3:137891675..137895635-chr3:137902725..137910565,16	MCF-7	breast:
4	chr3:137882800..137885689-chr3:137905079..137908377,3	MCF-7	breast:
5	chr3:137881170..137883124-chr3:137906116..137908266,2	K562	blood:
6	chr3:137889024..137895470-chr3:137896789..137909029,20	K562	blood:
7	chr12:3068006..3068677-chr3:137906028..137906625,2	Hela-S3	cervix:
8	chr3:137906153..137907747-chr3:138046736..138050249,3	MCF-7	breast:
9	chr3:137890311..137895409-chr3:137904718..137908692,8	MCF-7	breast:
10	chr3:137881624..137884175-chr3:137906260..137908266,2	K562	blood:

Variant related genes	Relation type
ARMC8	TF binding region
ENSG00000114098	Chromatin interaction
ENSG00000197905	Chromatin interaction
ENSG00000181322	Chromatin interaction
ENSG00000138231	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16847931	0.84[AFR][1000 genomes]
rs6789862	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7631817	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7637825	0.81[AMR][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	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2762347	chr3:137851198-137910007	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv998106	chr3:137851198-137934610	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv877536	chr3:137870523-137970907	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 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	chr3:137905000-137907200	Active TSS	Thymus	Thymus
2	chr3:137905200-137906800	Active TSS	Rectal Smooth Muscle	rectum
3	chr3:137905200-137907000	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:137905200-137907200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr3:137905200-137907200	Active TSS	Fetal Brain Female	brain
6	chr3:137905200-137907200	Active TSS	Fetal Lung	lung
7	chr3:137905200-137907400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:137905200-137907600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:137905200-137907800	Active TSS	Colonic Mucosa	Colon
10	chr3:137905400-137906600	ZNF genes & repeats	Fetal Brain Male	brain
11	chr3:137905400-137906800	Active TSS	Primary T cells fromperipheralblood	blood
12	chr3:137905400-137907200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr3:137905400-137907200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:137905400-137907200	Active TSS	Fetal Thymus	thymus
15	chr3:137905400-137907200	Active TSS	Stomach Smooth Muscle	stomach
16	chr3:137905400-137907400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr3:137905400-137907400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:137905400-137907400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:137905400-137907400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:137905400-137907400	Active TSS	Brain Hippocampus Middle	brain
21	chr3:137905400-137907400	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr3:137905400-137907600	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr3:137905400-137907600	Active TSS	NHLF	lung
24	chr3:137905400-137907800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr3:137905400-137907800	Active TSS	NHDF-Ad	bronchial
26	chr3:137905400-137908600	Active TSS	Psoas Muscle	Psoas
27	chr3:137905600-137906800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:137905600-137906800	Active TSS	Fetal Muscle Trunk	muscle
29	chr3:137905600-137907000	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr3:137905600-137907000	Active TSS	Liver	Liver
31	chr3:137905600-137907000	Active TSS	Fetal Muscle Leg	muscle
32	chr3:137905600-137907000	Active TSS	Placenta	Placenta
33	chr3:137905600-137907200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:137905600-137907200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:137905600-137907200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr3:137905600-137907200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:137905600-137907200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:137905600-137907200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:137905600-137907200	Active TSS	Brain Substantia Nigra	brain
40	chr3:137905600-137907200	Active TSS	Colon Smooth Muscle	Colon
41	chr3:137905600-137907200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr3:137905600-137907200	Active TSS	Fetal Kidney	kidney
43	chr3:137905600-137907200	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr3:137905600-137907200	Active TSS	Small Intestine	intestine
45	chr3:137905600-137907400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:137905600-137907400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:137905600-137907400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:137905600-137907400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:137905600-137907400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:137905600-137907400	Active TSS	Primary T killer memory cells from peripheral blood	blood

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