Variant report

Variant	rs3008616
Chromosome Location	chr1:222797173-222797174
allele	A/G
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	chr1:222797128-222797212	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222796724..222798547-chr1:222802534..222804355,2	MCF-7	breast:
2	chr1:222796161..222797805-chr1:222815899..222819162,3	MCF-7	breast:

Variant related genes	Relation type
MIA3	TF binding region
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1391557	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1391558	0.91[EUR][1000 genomes]
rs1498382	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17011666	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1909195	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2030076	0.81[EUR][1000 genomes]
rs2088514	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2133188	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2378604	0.81[EUR][1000 genomes]
rs2936020	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2936023	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2936049	0.89[EUR][1000 genomes]
rs2936051	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2936052	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2936054	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3002146	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3002148	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008614	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008615	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];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3008622	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3008625	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008629	0.83[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9441835	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9441926	0.84[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	chr1:222793000-222798800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:222793000-222799000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:222793000-222799800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:222793000-222800200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:222793000-222802200	Weak transcription	HSMMtube	muscle
14	chr1:222793200-222797600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:222793200-222797800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:222793200-222797800	Weak transcription	Fetal Lung	lung
17	chr1:222793200-222797800	Weak transcription	HUVEC	blood vessel
18	chr1:222793200-222798400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:222793200-222799400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:222793200-222799400	Weak transcription	Thymus	Thymus
21	chr1:222793200-222800000	Weak transcription	Pancreas	Pancrea
22	chr1:222793200-222800000	Weak transcription	Spleen	Spleen
23	chr1:222793200-222800000	Weak transcription	HMEC	breast
24	chr1:222793200-222800000	Weak transcription	NHLF	lung
25	chr1:222793200-222800200	Weak transcription	NHEK	skin
26	chr1:222793200-222800400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:222793200-222801000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:222793200-222801400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:222793200-222802200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:222793200-222802200	Weak transcription	Fetal Intestine Small	intestine
31	chr1:222793200-222802200	Weak transcription	Right Ventricle	heart
32	chr1:222793200-222802800	Weak transcription	Gastric	stomach
33	chr1:222793200-222816600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:222793200-222816600	Weak transcription	Hela-S3	cervix
35	chr1:222793400-222800000	Weak transcription	Brain Substantia Nigra	brain
36	chr1:222793600-222816600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:222793800-222797800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:222794000-222800600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:222794000-222806800	Strong transcription	Primary T cells from cord blood	blood
40	chr1:222794200-222797800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:222794200-222798400	Strong transcription	K562	blood
42	chr1:222794200-222802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:222794200-222805000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:222794400-222800000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:222794600-222800000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:222794600-222800000	Strong transcription	Liver	Liver
47	chr1:222794600-222801400	Weak transcription	GM12878-XiMat	blood
48	chr1:222794600-222803600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:222794600-222807200	Strong transcription	Fetal Thymus	thymus
50	chr1:222794600-222809800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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