Variant report

Variant	rs3741619
Chromosome Location	chr12:49389476-49389477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:161)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:161 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr12:49388935-49389591	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr12:49389360-49389510	HFF	foreskin:	n/a	n/a
3	RAD21	chr12:49389080-49389685	MCF-7	breast:	n/a	n/a
4	CTCF	chr12:49389139-49389552	A549	lung:	n/a	n/a
5	SMC3	chr12:49388909-49389765	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr12:49389211-49389551	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr12:49389234-49389543	Spleen_OC	spleen:	n/a	n/a
8	CTCF	chr12:49389136-49389496	A549	lung:	n/a	n/a
9	CTCF	chr12:49389360-49389510	A549	lung:	n/a	n/a
10	CTCF	chr12:49389171-49389528	A549	lung:	n/a	n/a
11	CTCF	chr12:49389074-49389562	K562	blood:	n/a	n/a
12	CTCF	chr12:49389160-49389530	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr12:49389340-49389490	WI-38	lung:	n/a	n/a
14	JUND	chr12:49389269-49389559	K562	blood:	n/a	n/a
15	CTCF	chr12:49389340-49389490	GM12871	blood:	n/a	n/a
16	RAD21	chr12:49389148-49389578	HepG2	liver:	n/a	n/a
17	CTCF	chr12:49389172-49389587	T-47D	breast:	n/a	n/a
18	RAD21	chr12:49389166-49389592	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr12:49389360-49389510	NHDF-neo	bronchial:	n/a	n/a
20	CTCF	chr12:49389340-49389490	HRE	kidney:	n/a	n/a
21	SMC3	chr12:49389206-49389560	GM12878	blood:	n/a	n/a
22	RAD21	chr12:49389177-49389554	GM12878	blood:	n/a	n/a
23	MAX	chr12:49389374-49389487	GM12878	blood:	n/a	n/a
24	CTCF	chr12:49389246-49389511	LNCaP	prostate:	n/a	n/a
25	MXI1	chr12:49389157-49389526	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr12:49389131-49389535	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr12:49388938-49389858	HCT-116	colon:	n/a	n/a
28	CTCF	chr12:49389340-49389490	GM12864	blood:	n/a	n/a
29	CTCF	chr12:49389107-49389613	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD1	chr12:49389344-49389646	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr12:49389231-49389521	NHEK	skin:	n/a	n/a
32	RAD21	chr12:49389169-49389646	ECC-1	luminal epithelium:	n/a	n/a
33	CTCF	chr12:49389340-49389490	A549	lung:	n/a	n/a
34	CTCF	chr12:49389269-49389505	MCF-7	breast:	n/a	n/a
35	RAD21	chr12:49389197-49389556	A549	lung:	n/a	n/a
36	POLR2A	chr12:49389097-49389565	SK-N-MC	brain:	n/a	n/a
37	CTCF	chr12:49389259-49389509	Lung_OC	lung:	n/a	n/a
38	CTCF	chr12:49389277-49389485	GM13976	blood:	n/a	n/a
39	CTCF	chr12:49389294-49389506	GM20000	blood:	n/a	n/a
40	MYC	chr12:49389309-49389657	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr12:49389251-49389516	GM19239	blood:	n/a	n/a
42	CTCF	chr12:49389270-49389497	HepG2	liver:	n/a	n/a
43	TEAD4	chr12:49389211-49389680	H1-hESC	embryonic stem cell:	n/a	n/a
44	CHD2	chr12:49389202-49389488	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr12:49389241-49389526	MCF-7	breast:	n/a	n/a
46	RAD21	chr12:49389037-49389703	A549	lung:	n/a	n/a
47	RAD21	chr12:49389067-49389690	MCF-7	breast:	n/a	n/a
48	RCOR1	chr12:49388996-49389533	K562	blood:	n/a	n/a
49	CTCF	chr12:49389216-49389560	GM12892	blood:	n/a	n/a
50	MAZ	chr12:49389185-49389526	K562	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49370543..49373211-chr12:49387729..49389906,2	K562	blood:
2	chr12:49329635..49330325-chr12:49389189..49389770,2	MCF-7	breast:
3	chr12:49365293..49369225-chr12:49386844..49389863,3	MCF-7	breast:
4	chr12:49211500..49213760-chr12:49389439..49391048,2	MCF-7	breast:
5	chr12:49371444..49371981-chr12:49389232..49389805,2	K562	blood:
6	chr12:49366496..49367129-chr12:49388953..49389723,2	MCF-7	breast:
7	chr12:49349915..49351718-chr12:49389253..49391123,2	MCF-7	breast:
8	chr12:49327871..49328779-chr12:49389340..49389872,3	MCF-7	breast:
9	chr12:49370543..49373352-chr12:49387358..49390310,3	K562	blood:
10	chr12:49389429..49391969-chr12:49402571..49406442,3	MCF-7	breast:
11	chr12:49389470..49393018-chr12:49447976..49450275,4	K562	blood:
12	chr12:49246756..49247834-chr12:49389266..49390145,3	K562	blood:
13	chr12:49367970..49369759-chr12:49389429..49392396,2	K562	blood:
14	chr12:49374060..49376020-chr12:49389393..49391563,2	K562	blood:
15	chr12:49367583..49368499-chr12:49388939..49389819,2	K562	blood:
16	chr12:49388997..49391311-chr12:49485672..49487857,2	K562	blood:
17	chr12:49350460..49352797-chr12:49389222..49392992,4	MCF-7	breast:
18	chr12:49388402..49390811-chr12:49410964..49413711,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257913	TF binding region
ENSG00000200303	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000125084	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000181929	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1054442	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747559	0.81[ASN][1000 genomes]
rs10783299	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs10783300	0.95[ASN][1000 genomes]
rs10783301	0.85[ASN][1000 genomes]
rs10875906	0.99[ASN][1000 genomes]
rs10875908	0.95[ASN][1000 genomes]
rs10875910	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875911	0.95[ASN][1000 genomes]
rs10875912	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875913	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875914	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs10875915	0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11168822	0.92[ASN][1000 genomes]
rs11168827	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168839	0.89[ASW][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs11168850	1.00[JPT][hapmap];0.80[YRI][hapmap]
rs1138908	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11614738	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12580349	0.90[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2117029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2241726	0.89[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2293445	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[ASN][1000 genomes]
rs2293446	0.94[ASN][1000 genomes]
rs2304275	0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34436857	0.85[ASN][1000 genomes]
rs3741622	0.89[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3782357	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6580698	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6580699	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7296288	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7969091	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs876333	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49388200-49390000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
2	chr12:49388200-49390600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:49388200-49393600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:49388400-49389800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:49388600-49389600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:49388600-49390400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:49388800-49389600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:49388800-49389600	Bivalent Enhancer	Fetal Thymus	thymus
9	chr12:49388800-49389600	Bivalent Enhancer	NH-A	brain
10	chr12:49388800-49389800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:49388800-49389800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:49388800-49389800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr12:49388800-49390400	Bivalent Enhancer	Brain Germinal Matrix	brain
14	chr12:49389000-49389600	Bivalent Enhancer	Primary B cells from cord blood	blood
15	chr12:49389000-49389600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr12:49389000-49389600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr12:49389000-49389600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:49389000-49389600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
19	chr12:49389000-49390200	Bivalent Enhancer	Fetal Kidney	kidney
20	chr12:49389200-49389600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
21	chr12:49389200-49389600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:49389200-49389800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr12:49389200-49389800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
24	chr12:49389200-49389800	Enhancers	Esophagus	oesophagus
25	chr12:49389200-49389800	Bivalent Enhancer	Fetal Intestine Small	intestine
26	chr12:49389200-49390000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr12:49389200-49390000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
28	chr12:49389200-49390800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:49389200-49390800	Weak transcription	Pancreas	Pancrea
30	chr12:49389400-49389600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
31	chr12:49389400-49389600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:49389400-49389600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:49389400-49389600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:49389400-49389600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:49389400-49389600	Bivalent Enhancer	Adipose Nuclei	Adipose
36	chr12:49389400-49389600	Weak transcription	Brain Anterior Caudate	brain
37	chr12:49389400-49389600	Bivalent Enhancer	Stomach Mucosa	stomach
38	chr12:49389400-49389800	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:49389400-49389800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr12:49389400-49389800	Bivalent Enhancer	Placenta	Placenta
41	chr12:49389400-49389800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
42	chr12:49389400-49389800	Enhancers	Hela-S3	cervix
43	chr12:49389400-49390000	Weak transcription	Right Atrium	heart
44	chr12:49389400-49390200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:49389400-49390200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:49389400-49390400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:49389400-49390400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:49389400-49390400	Enhancers	Brain Hippocampus Middle	brain
49	chr12:49389400-49390400	Weak transcription	Brain Substantia Nigra	brain
50	chr12:49389400-49390400	Weak transcription	K562	blood

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