Variant report

Variant	rs7913612
Chromosome Location	chr10:49702415-49702416
allele	C/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	POLR2A	chr10:49701733-49702908	U87	brain:	n/a	n/a
2	MAX	chr10:49701725-49702511	K562	blood:	n/a	chr10:49702017-49702027 chr10:49702001-49702010
3	ELF1	chr10:49702204-49702523	K562	blood:	n/a	chr10:49702371-49702384
4	POLR2A	chr10:49701892-49702824	U87	brain:	n/a	n/a

Variant related genes	Relation type
ARHGAP22	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10735226	0.93[LWK][hapmap];0.82[MKK][hapmap];0.85[AFR][1000 genomes]
rs10745277	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10776607	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10776609	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10776610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857585	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857586	0.90[ASN][1000 genomes]
rs10857590	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11101343	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11101358	0.88[ASN][1000 genomes]
rs11101370	0.89[CHD][hapmap];0.89[JPT][hapmap]
rs11101371	0.89[CHD][hapmap];0.89[JPT][hapmap]
rs12249815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12265171	0.85[ASN][1000 genomes]
rs1814471	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867582	0.91[ASN][1000 genomes]
rs1947075	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs2377354	0.82[JPT][hapmap]
rs4575219	0.82[EUR][1000 genomes]
rs4838412	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4838417	0.83[JPT][hapmap]
rs4838607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4838611	0.85[ASN][1000 genomes]
rs7913593	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9663790	0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv467191	chr10:49669142-49735563	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv550813	chr10:49669142-49735563	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7913612	ANTXRL	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49679800-49704200	Weak transcription	NH-A	brain
2	chr10:49679800-49704200	Weak transcription	NHDF-Ad	bronchial
3	chr10:49685800-49704800	Weak transcription	HUVEC	blood vessel
4	chr10:49687000-49704400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:49687600-49703800	Weak transcription	HSMMtube	muscle
6	chr10:49696800-49702600	Weak transcription	HSMM	muscle
7	chr10:49698000-49731200	Weak transcription	Aorta	Aorta
8	chr10:49698200-49702600	Enhancers	Brain Substantia Nigra	brain
9	chr10:49698400-49703800	Enhancers	Primary hematopoietic stem cells	blood
10	chr10:49699200-49705200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:49699200-49706000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:49699200-49706400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:49699400-49705200	Weak transcription	Brain Anterior Caudate	brain
14	chr10:49699800-49704800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr10:49700400-49704200	Enhancers	Fetal Thymus	thymus
16	chr10:49700600-49702600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr10:49700600-49706800	Enhancers	K562	blood
18	chr10:49701000-49703000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:49701000-49703000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr10:49701000-49703400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr10:49701000-49703400	Enhancers	NHEK	skin
22	chr10:49701000-49703800	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr10:49701200-49703200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:49701400-49702600	Enhancers	Brain Hippocampus Middle	brain
25	chr10:49701400-49703000	Enhancers	Primary T cells from cord blood	blood
26	chr10:49701400-49706000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:49701400-49706000	Enhancers	HMEC	breast
28	chr10:49701600-49702600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr10:49701600-49703000	Enhancers	Thymus	Thymus
30	chr10:49701600-49716400	Weak transcription	Right Atrium	heart
31	chr10:49701800-49703200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:49701800-49703200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr10:49702000-49702800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr10:49702000-49702800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr10:49702000-49703000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr10:49702000-49704800	Weak transcription	Osteobl	bone
37	chr10:49702000-49705000	Weak transcription	Brain Angular Gyrus	brain
38	chr10:49702200-49702600	Enhancers	Dnd41	blood
39	chr10:49702200-49703000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr10:49702200-49704600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr10:49702200-49705800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr10:49702200-49707400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr10:49702400-49702600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr10:49702400-49703400	Weak transcription	Placenta	Placenta
45	chr10:49702400-49703800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr10:49702400-49704200	Weak transcription	NHLF	lung
47	chr10:49702400-49704600	Weak transcription	Esophagus	oesophagus
48	chr10:49702400-49718200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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