Variant report

Variant	rs6670216
Chromosome Location	chr1:77686596-77686597
allele	G/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	STAT3	chr1:77686416-77686803	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:77686415-77686673	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr1:77686303-77686696	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr1:77686365-77686777	Hela-S3	cervix:	n/a	n/a
5	FOS	chr1:77686417-77686808	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:77686393-77686803	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr1:77686262-77686762	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr1:77686415-77686810	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr1:77686337-77686744	IMR90	lung:	n/a	n/a
10	STAT3	chr1:77686350-77686801	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr1:77686413-77686747	A549	lung:	n/a	n/a
12	STAT3	chr1:77686391-77686830	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr1:77686298-77686827	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:77686353-77686833	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77684670..77686781-chr1:77746398..77749229,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AK5-1	chr1:77686473-77686671	XLOC_000263
2	lnc-AK5-1	chr1:77686286-77690011	NONHSAT004022

Variant related genes	Relation type
PIGK	TF binding region
ENSG00000154027	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11162269	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11162270	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11162272	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11162277	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162278	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162279	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11162280	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11162281	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162291	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11487923	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11807652	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12059517	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12060044	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12071267	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083834	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12086383	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12093439	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12401794	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12403340	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12406806	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12410452	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12569172	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1608507	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1916692	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979883	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs199712	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2055479	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2134353	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2177429	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34052737	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35762413	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4397697	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949648	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4949650	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949651	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4949769	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4949774	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949776	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57907490	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6683950	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72992503	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524874	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7531782	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7531970	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9787278	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919302	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][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	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong 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:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77684000-77686600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:77684600-77686800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:77685200-77687000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:77685200-77687800	Weak transcription	Spleen	Spleen
5	chr1:77685400-77688000	Weak transcription	Gastric	stomach
6	chr1:77685400-77689600	Weak transcription	Esophagus	oesophagus
7	chr1:77685600-77686600	Flanking Active TSS	Dnd41	blood
8	chr1:77685600-77693400	Weak transcription	Pancreas	Pancrea
9	chr1:77685800-77686600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:77685800-77686600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:77685800-77686600	Enhancers	Liver	Liver
12	chr1:77685800-77686600	Weak transcription	Hela-S3	cervix
13	chr1:77685800-77686600	Flanking Active TSS	HUVEC	blood vessel
14	chr1:77685800-77686800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:77685800-77687600	Weak transcription	Fetal Stomach	stomach
16	chr1:77685800-77687800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:77685800-77687800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:77685800-77687800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:77685800-77687800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:77685800-77687800	Weak transcription	Aorta	Aorta
21	chr1:77685800-77688400	Weak transcription	Right Atrium	heart
22	chr1:77685800-77688600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:77685800-77688600	Weak transcription	Fetal Thymus	thymus
24	chr1:77685800-77688600	Weak transcription	Psoas Muscle	Psoas
25	chr1:77685800-77688800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:77685800-77689000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:77685800-77689600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:77685800-77689600	Weak transcription	Ovary	ovary
29	chr1:77685800-77690000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:77685800-77692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:77685800-77695600	Weak transcription	Left Ventricle	heart
32	chr1:77686000-77686600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:77686000-77686600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:77686000-77686600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:77686000-77686600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr1:77686000-77686600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr1:77686000-77686600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:77686000-77686600	Enhancers	Brain Hippocampus Middle	brain
39	chr1:77686000-77686600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:77686000-77686600	Enhancers	NHEK	skin
41	chr1:77686000-77686800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:77686000-77686800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:77686000-77686800	Enhancers	NH-A	brain
44	chr1:77686000-77687000	Enhancers	Brain Substantia Nigra	brain
45	chr1:77686000-77687400	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:77686000-77687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:77686000-77688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:77686000-77688000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:77686000-77688000	Weak transcription	Fetal Intestine Large	intestine
50	chr1:77686000-77688000	Weak transcription	Fetal Intestine Small	intestine

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