Variant report

Variant	rs1980191
Chromosome Location	chr3:141456675-141456676
allele	A/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	ARID3A	chr3:141456675-141457295	K562	blood:	n/a	n/a
2	SIN3AK20	chr3:141456560-141458361	MCF-7	breast:	n/a	n/a
3	JUND	chr3:141456524-141457709	GM12878	blood:	n/a	chr3:141456990-141456999 chr3:141457015-141457024
4	RAD21	chr3:141456427-141458407	SK-N-SH	brain:	n/a	chr3:141456992-141457002 chr3:141457004-141457017 chr3:141457531-141457544
5	POLR2A	chr3:141456637-141458013	GM12892	blood:	n/a	n/a
6	RAD21	chr3:141456648-141457937	HCT-116	colon:	n/a	chr3:141456992-141457002 chr3:141457004-141457017 chr3:141457531-141457544
7	SP1	chr3:141456495-141457582	HCT-116	colon:	n/a	chr3:141456975-141456986 chr3:141456987-141456998 chr3:141456975-141456987 chr3:141456976-141456985 chr3:141456975-141456987 chr3:141456977-141456986 chr3:141456976-141456986 chr3:141456989-141456998
8	POLR2A	chr3:141456606-141457626	U87	brain:	n/a	n/a
9	NRF1	chr3:141456493-141457521	SK-N-SH	brain:	n/a	chr3:141456879-141456890 chr3:141456880-141456894 chr3:141456877-141456891
10	RCOR1	chr3:141456628-141458176	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr3:141456670-141457743	MCF-7	breast:	n/a	n/a
12	RUNX3	chr3:141456578-141458042	GM12878	blood:	n/a	n/a
13	FOXM1	chr3:141456593-141457546	GM12878	blood:	n/a	n/a
14	MYBL2	chr3:141456506-141457459	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:141456573-141457631	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr3:141456669-141458042	GM18526	blood:	n/a	n/a
17	POLR2A	chr3:141456617-141458146	MCF-7	breast:	n/a	n/a
18	RFX5	chr3:141456660-141457315	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:141456626-141457508	GM12878	blood:	n/a	n/a
20	SP1	chr3:141456658-141457756	A549	lung:	n/a	chr3:141456975-141456986 chr3:141456987-141456998 chr3:141456975-141456987 chr3:141456976-141456985 chr3:141456975-141456987 chr3:141456977-141456986 chr3:141456976-141456986 chr3:141456989-141456998
21	CREB1	chr3:141456593-141457915	K562	blood:	n/a	chr3:141457013-141457026
22	MAX	chr3:141456587-141458199	A549	lung:	n/a	chr3:141456976-141456986
23	CEBPB	chr3:141456591-141457283	ECC-1	luminal epithelium:	n/a	chr3:141457036-141457044
24	POLR2A	chr3:141456642-141457411	ECC-1	luminal epithelium:	n/a	n/a
25	USF2	chr3:141456604-141457331	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:141456670-141458092	GM18951	blood:	n/a	n/a
27	CREB1	chr3:141456622-141457561	H1-hESC	embryonic stem cell:	n/a	chr3:141457013-141457026
28	GATA3	chr3:141456605-141457657	T-47D	breast:	n/a	n/a
29	RAD21	chr3:141456503-141457663	HCT-116	colon:	n/a	chr3:141456992-141457002 chr3:141457004-141457017 chr3:141457531-141457544
30	TAF1	chr3:141456646-141457551	GM12878	blood:	n/a	n/a
31	YY1	chr3:141456667-141458491	SK-N-SH	brain:	n/a	chr3:141457539-141457553 chr3:141456973-141456987 chr3:141457545-141457554 chr3:141458092-141458108 chr3:141457556-141457567 chr3:141457540-141457554
32	CTCF	chr3:141456640-141456790	HCPEpiC	choroid plexus:	n/a	n/a
33	STAT3	chr3:141456570-141457152	MCF10A-Er-Src	breast:	n/a	n/a
34	TBP	chr3:141456634-141457393	GM12878	blood:	n/a	n/a
35	MAX	chr3:141456638-141457534	GM12878	blood:	n/a	chr3:141456976-141456986
36	MAZ	chr3:141456590-141458430	IMR90	lung:	n/a	chr3:141456976-141456986
37	POLR2A	chr3:141456635-141457550	H1-neurons	neurons:	n/a	n/a
38	NFIC	chr3:141456648-141457217	HepG2	liver:	n/a	n/a
39	POLR2A	chr3:141456627-141458002	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr3:141456660-141457638	A549	lung:	n/a	n/a
41	CREB1	chr3:141456524-141457526	K562	blood:	n/a	chr3:141457013-141457026
42	MAX	chr3:141456573-141458287	A549	lung:	n/a	chr3:141456976-141456986
43	BCL3	chr3:141456640-141457202	A549	lung:	n/a	chr3:141456901-141456914
44	ATF2	chr3:141456623-141457298	H1-hESC	embryonic stem cell:	n/a	chr3:141457014-141457025 chr3:141457012-141457026
45	MYBL2	chr3:141456573-141457673	HepG2	liver:	n/a	n/a
46	POLR2A	chr3:141456647-141457449	PFSK-1	brain:	n/a	n/a
47	CREB1	chr3:141456647-141457802	HepG2	liver:	n/a	chr3:141457013-141457026
48	MXI1	chr3:141456382-141459033	IMR90	lung:	n/a	n/a
49	POLR2A	chr3:141456648-141457677	HCT-116	colon:	n/a	n/a
50	CREB1	chr3:141456627-141457561	GM12878	blood:	n/a	chr3:141457013-141457026

No.	Distal block	Cell Line	Cell type
1	chr3:141455674..141460093-chr3:141592801..141597430,19	MCF-7	breast:
2	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:
3	chr3:141357032..141359290-chr3:141454667..141456901,2	K562	blood:
4	chr3:141456656..141457567-chr3:141593967..141595178,5	K562	blood:
5	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
6	chr3:141456347..141457648-chr3:141594019..141595007,11	MCF-7	breast:
7	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
8	chr3:141455584..141459326-chr3:141464266..141467931,6	MCF-7	breast:
9	chr3:141456324..141457198-chr3:141594736..141595366,2	Hela-S3	cervix:

Variant related genes	Relation type
RNF7	TF binding region
ENSG00000069849	Chromatin interaction
ENSG00000114125	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1105082	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16851704	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1980192	0.98[ASN][1000 genomes]
rs59998648	0.88[ASN][1000 genomes]
rs60806348	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61632965	0.88[ASN][1000 genomes]
rs73226647	0.84[EUR][1000 genomes]
rs7630533	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs868934	0.82[CHB][hapmap]
rs9789959	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877552	chr3:141420562-141466147	Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141455000-141457000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:141456000-141457000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr3:141456200-141457800	Active TSS	Primary T cells from cord blood	blood
4	chr3:141456400-141457000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
5	chr3:141456400-141457200	Active TSS	HepG2	liver
6	chr3:141456400-141458200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:141456600-141456800	Flanking Active TSS	Primary B cells from peripheral blood	blood
8	chr3:141456600-141456800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr3:141456600-141456800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr3:141456600-141456800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr3:141456600-141456800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:141456600-141456800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:141456600-141456800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr3:141456600-141456800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr3:141456600-141456800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:141456600-141456800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:141456600-141456800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr3:141456600-141456800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr3:141456600-141456800	Flanking Active TSS	Fetal Intestine Large	intestine
20	chr3:141456600-141456800	Flanking Active TSS	Fetal Thymus	thymus
21	chr3:141456600-141456800	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr3:141456600-141456800	Flanking Active TSS	Dnd41	blood
23	chr3:141456600-141456800	Flanking Active TSS	GM12878-XiMat	blood
24	chr3:141456600-141456800	Flanking Active TSS	K562	blood
25	chr3:141456600-141456800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr3:141456600-141456800	Flanking Active TSS	NHLF	lung
27	chr3:141456600-141457000	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr3:141456600-141457000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:141456600-141457200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr3:141456600-141457200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:141456600-141457200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:141456600-141457200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:141456600-141457600	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:141456600-141457800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:141456600-141457800	Active TSS	Adipose Nuclei	Adipose
36	chr3:141456600-141457800	Active TSS	Liver	Liver
37	chr3:141456600-141458000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:141456600-141458000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:141456600-141458000	Active TSS	Fetal Heart	heart
40	chr3:141456600-141458200	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr3:141456600-141458200	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr3:141456600-141458200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr3:141456600-141458200	Active TSS	Brain Cingulate Gyrus	brain
44	chr3:141456600-141458200	Active TSS	Colon Smooth Muscle	Colon
45	chr3:141456600-141458200	Active TSS	Left Ventricle	heart
46	chr3:141456600-141458200	Active TSS	Placenta Amnion	Placenta Amnion
47	chr3:141456600-141458200	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr3:141456600-141458200	Active TSS	Stomach Mucosa	stomach
49	chr3:141456600-141458200	Active TSS	Hela-S3	cervix
50	chr3:141456600-141458200	Active TSS	Osteobl	bone

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