Variant report

Variant	rs3008615
Chromosome Location	chr1:222796584-222796585
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222796161..222797805-chr1:222815899..222819162,3	MCF-7	breast:
2	chr1:222713330..222714959-chr1:222794373..222797061,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143512	Chromatin interaction
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1391557	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1391558	0.91[EUR][1000 genomes]
rs1498382	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17011666	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1909195	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1909197	0.80[AMR][1000 genomes]
rs2030076	0.81[EUR][1000 genomes]
rs2088514	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2133188	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2378604	0.81[EUR][1000 genomes]
rs2936020	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2936023	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2936049	0.89[EUR][1000 genomes]
rs2936051	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2936052	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2936054	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3002146	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3002148	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008616	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008618	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3008622	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3008625	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008629	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3008637	0.89[EUR][1000 genomes]
rs34433664	0.82[EUR][1000 genomes]
rs3811465	0.82[EUR][1000 genomes]
rs61827168	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9441835	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9441926	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222792400-222816600	Weak transcription	Small Intestine	intestine
2	chr1:222792600-222800000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:222792600-222801400	Weak transcription	Lung	lung
4	chr1:222792600-222802200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:222792600-222802200	Weak transcription	Aorta	Aorta
6	chr1:222792600-222816600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:222792600-222817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:222792800-222802000	Weak transcription	Colonic Mucosa	Colon
9	chr1:222793000-222797000	Weak transcription	Fetal Intestine Large	intestine
10	chr1:222793000-222798800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:222793000-222799000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:222793000-222799800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:222793000-222800200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:222793000-222802200	Weak transcription	HSMMtube	muscle
15	chr1:222793200-222796800	Weak transcription	Fetal Heart	heart
16	chr1:222793200-222797600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:222793200-222797800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:222793200-222797800	Weak transcription	Fetal Lung	lung
19	chr1:222793200-222797800	Weak transcription	HUVEC	blood vessel
20	chr1:222793200-222798400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:222793200-222799400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:222793200-222799400	Weak transcription	Thymus	Thymus
23	chr1:222793200-222800000	Weak transcription	Pancreas	Pancrea
24	chr1:222793200-222800000	Weak transcription	Spleen	Spleen
25	chr1:222793200-222800000	Weak transcription	HMEC	breast
26	chr1:222793200-222800000	Weak transcription	NHLF	lung
27	chr1:222793200-222800200	Weak transcription	NHEK	skin
28	chr1:222793200-222800400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:222793200-222801000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:222793200-222801400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:222793200-222802200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:222793200-222802200	Weak transcription	Fetal Intestine Small	intestine
33	chr1:222793200-222802200	Weak transcription	Right Ventricle	heart
34	chr1:222793200-222802800	Weak transcription	Gastric	stomach
35	chr1:222793200-222816600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:222793200-222816600	Weak transcription	Hela-S3	cervix
37	chr1:222793400-222800000	Weak transcription	Brain Substantia Nigra	brain
38	chr1:222793600-222816600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:222793800-222797800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:222794000-222800600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:222794000-222806800	Strong transcription	Primary T cells from cord blood	blood
42	chr1:222794200-222797800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:222794200-222798400	Strong transcription	K562	blood
44	chr1:222794200-222802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:222794200-222805000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:222794400-222800000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:222794600-222796600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:222794600-222797000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:222794600-222800000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:222794600-222800000	Strong transcription	Liver	Liver

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