Variant report

Variant	rs2970469
Chromosome Location	chr7:101471055-101471056
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	POLR2A	chr7:101470817-101471158	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:101468629..101471194-chr7:101478234..101481000,2	K562	blood:
2	chr7:101461830..101464614-chr7:101470507..101472083,2	K562	blood:
3	chr7:101466687..101469214-chr7:101470769..101472516,2	K562	blood:
4	chr7:101469683..101471834-chr7:101546333..101548097,2	K562	blood:

Variant related genes	Relation type
ENSG00000259294	TF binding region
ENSG00000257923	Chromatin interaction
ENSG00000259294	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10270083	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2906717	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906719	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906741	0.80[AMR][1000 genomes]
rs2906743	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906745	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906746	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2906747	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906748	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970461	0.98[EUR][1000 genomes]
rs2970462	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970464	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970465	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970466	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970467	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970470	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970495	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs4236558	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs4354243	1.00[JPT][hapmap]
rs73183694	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv824243	chr7:101445202-101479651	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv521041	chr7:101458144-101496391	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2970469	ARPC1B	cis	cerebellum	SCAN
rs2970469	ACHE	cis	lymphoblastoid	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101461200-101471800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:101461200-101475200	Weak transcription	Esophagus	oesophagus
3	chr7:101461200-101475400	Weak transcription	Colonic Mucosa	Colon
4	chr7:101461200-101475400	Weak transcription	Gastric	stomach
5	chr7:101461200-101486200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:101461400-101471400	Weak transcription	Primary T cells from cord blood	blood
7	chr7:101461400-101473000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:101461800-101477000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:101461800-101489200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:101462000-101477000	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:101462200-101472600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:101462200-101473200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:101462200-101482200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:101462200-101484200	Weak transcription	Fetal Kidney	kidney
15	chr7:101462400-101474200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr7:101462600-101471400	Weak transcription	Osteobl	bone
17	chr7:101462800-101471800	Weak transcription	Primary B cells from cord blood	blood
18	chr7:101462800-101471800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:101463800-101489800	Weak transcription	NHEK	skin
20	chr7:101464400-101472000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:101464400-101478400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:101464600-101488800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:101465800-101482000	Weak transcription	K562	blood
24	chr7:101466800-101471200	Weak transcription	GM12878-XiMat	blood
25	chr7:101466800-101471600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:101466800-101482200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:101466800-101489800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:101466800-101498400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:101467000-101471400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:101467000-101471800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr7:101467000-101473000	Weak transcription	Fetal Muscle Leg	muscle
32	chr7:101467000-101480200	Weak transcription	Aorta	Aorta
33	chr7:101467000-101480200	Weak transcription	Pancreas	Pancrea
34	chr7:101467000-101480600	Weak transcription	HSMM	muscle
35	chr7:101467000-101482000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:101467200-101472400	Weak transcription	Hela-S3	cervix
37	chr7:101467200-101473200	Weak transcription	Adipose Nuclei	Adipose
38	chr7:101467200-101475400	Weak transcription	Stomach Mucosa	stomach
39	chr7:101467200-101477000	Weak transcription	Brain Substantia Nigra	brain
40	chr7:101467200-101481800	Weak transcription	Liver	Liver
41	chr7:101467200-101490400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:101467400-101475400	Weak transcription	A549	lung
43	chr7:101467400-101490400	Weak transcription	Fetal Lung	lung
44	chr7:101467600-101474200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr7:101467600-101476800	Strong transcription	Fetal Intestine Small	intestine
46	chr7:101468000-101471400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr7:101468800-101471800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr7:101468800-101486600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr7:101469000-101472000	Weak transcription	Psoas Muscle	Psoas
50	chr7:101469000-101472400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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