Variant report

Variant	rs12210597
Chromosome Location	chr6:57077135-57077136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:57076789..57078523-chr6:57080128..57081654,2	K562	blood:
2	chr6:57074492..57078163-chr6:57083348..57087890,4	K562	blood:

Variant related genes	Relation type
ENSG00000112210	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1157713	0.80[ASN][1000 genomes]
rs12190416	0.80[ASN][1000 genomes]
rs12190434	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12192711	0.96[ASN][1000 genomes]
rs12211611	0.82[CEU][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16888392	0.81[CEU][hapmap]
rs2273921	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3734738	0.96[ASN][1000 genomes]
rs3778515	0.96[ASN][1000 genomes]
rs3800018	0.81[CEU][hapmap]
rs3800019	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3996929	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6459180	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6913707	0.85[ASN][1000 genomes]
rs6926980	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6928715	0.96[ASN][1000 genomes]
rs6929783	0.85[ASN][1000 genomes]
rs6936472	0.93[ASN][1000 genomes]
rs7744316	1.00[CEU][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744824	0.94[ASN][1000 genomes]
rs7753537	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7763570	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8180538	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9349843	0.93[ASN][1000 genomes]
rs9367708	0.93[ASN][1000 genomes]
rs9370564	0.93[ASN][1000 genomes]
rs9370565	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9382689	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9396259	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs952647	0.93[ASN][1000 genomes]
rs9885757	0.96[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12210597	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs12210597	BEND6	cis	Skin Sun Exposed Lower leg	GTEx
rs12210597	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57038000-57081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:57038400-57079600	Weak transcription	Fetal Brain Female	brain
3	chr6:57039000-57086000	Weak transcription	Thymus	Thymus
4	chr6:57049400-57085000	Weak transcription	Aorta	Aorta
5	chr6:57056600-57086000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:57057200-57081200	Weak transcription	HMEC	breast
7	chr6:57057600-57081200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:57058000-57080800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:57058200-57079200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:57058200-57085800	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:57058400-57078800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:57058800-57081000	Weak transcription	NHEK	skin
13	chr6:57058800-57084000	Weak transcription	Dnd41	blood
14	chr6:57059200-57084000	Weak transcription	Hela-S3	cervix
15	chr6:57060600-57080600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:57061600-57079600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:57062600-57084800	Weak transcription	HSMM	muscle
18	chr6:57064200-57077800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:57064400-57077400	Weak transcription	Fetal Stomach	stomach
20	chr6:57064400-57077400	Weak transcription	HepG2	liver
21	chr6:57064400-57079000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:57064400-57079400	Weak transcription	NHLF	lung
23	chr6:57064400-57084000	Weak transcription	NH-A	brain
24	chr6:57064400-57085000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:57064400-57086200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:57065000-57085000	Weak transcription	A549	lung
27	chr6:57067400-57078600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:57067600-57085800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:57070600-57086000	Weak transcription	HSMMtube	muscle
30	chr6:57071600-57079000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:57071600-57084800	Weak transcription	HUVEC	blood vessel
32	chr6:57071800-57079400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:57071800-57080800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:57072000-57078600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:57072000-57085800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:57072200-57081000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:57073200-57078800	Weak transcription	GM12878-XiMat	blood
38	chr6:57073200-57081200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:57073600-57079200	Weak transcription	Osteobl	bone
40	chr6:57073600-57081400	Weak transcription	NHDF-Ad	bronchial
41	chr6:57073800-57077200	Enhancers	Colon Smooth Muscle	Colon
42	chr6:57073800-57080800	Weak transcription	Fetal Lung	lung
43	chr6:57073800-57081200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:57074000-57078000	Weak transcription	K562	blood
45	chr6:57075000-57078200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:57075800-57080000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:57076000-57079400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:57076400-57077400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:57076800-57078200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:57077000-57078600	Weak transcription	Rectal Smooth Muscle	rectum

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