Variant report

Variant	rs9885757
Chromosome Location	chr6:57048458-57048459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:57045877..57048484-chr6:57055538..57057146,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1157713	0.93[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190416	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192711	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210597	0.96[ASN][1000 genomes]
rs12211611	0.88[CHB][hapmap];1.00[ASN][1000 genomes]
rs2100305	0.80[ASN][1000 genomes]
rs2273921	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734738	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778515	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800019	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3996929	0.84[ASN][1000 genomes]
rs3996933	0.80[ASN][1000 genomes]
rs3996937	0.82[ASN][1000 genomes]
rs4715646	0.80[ASN][1000 genomes]
rs6459180	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6913707	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6928715	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929783	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6936472	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7743855	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs7744316	1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[ASN][1000 genomes]
rs7744824	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753537	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753927	0.93[ASW][hapmap];0.86[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.80[ASN][1000 genomes]
rs7763570	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180538	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349843	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367704	0.93[CEU][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9367708	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9370564	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370565	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382689	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396259	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952647	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];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
rs9885757	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs9885757	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs9885757	BEND6	cis	Muscle Skeletal	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57038000-57054200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:57038000-57056000	Weak transcription	Spleen	Spleen
3	chr6:57038000-57081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:57038200-57051200	Weak transcription	Small Intestine	intestine
5	chr6:57038200-57063800	Weak transcription	Esophagus	oesophagus
6	chr6:57038200-57063800	Weak transcription	Gastric	stomach
7	chr6:57038400-57056200	Weak transcription	Brain Germinal Matrix	brain
8	chr6:57038400-57072800	Weak transcription	Pancreas	Pancrea
9	chr6:57038400-57079600	Weak transcription	Fetal Brain Female	brain
10	chr6:57038600-57049800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:57038600-57064000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:57038800-57056400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:57038800-57060400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:57039000-57049400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:57039000-57050000	Weak transcription	Brain Substantia Nigra	brain
16	chr6:57039000-57056400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:57039000-57086000	Weak transcription	Thymus	Thymus
18	chr6:57039200-57054200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:57039200-57056200	Weak transcription	Fetal Intestine Small	intestine
20	chr6:57039400-57052000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:57039400-57052200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:57039400-57056200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:57039600-57050400	Weak transcription	NHEK	skin
24	chr6:57039600-57064000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:57039800-57048600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:57041400-57050400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:57041600-57049800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:57042200-57064000	Weak transcription	Colonic Mucosa	Colon
29	chr6:57042800-57060400	Weak transcription	Right Ventricle	heart
30	chr6:57043000-57051000	Strong transcription	K562	blood
31	chr6:57043200-57048600	Weak transcription	Psoas Muscle	Psoas
32	chr6:57043200-57049600	Strong transcription	Hela-S3	cervix
33	chr6:57043400-57050000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:57043800-57049800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:57043800-57063800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:57044000-57056200	Strong transcription	A549	lung
37	chr6:57044000-57057600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:57044400-57054200	Strong transcription	NHDF-Ad	bronchial
39	chr6:57044400-57059000	Strong transcription	Osteobl	bone
40	chr6:57044600-57054400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:57045200-57051000	Strong transcription	Dnd41	blood
42	chr6:57045400-57050800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:57045400-57052600	Strong transcription	NH-A	brain
44	chr6:57045400-57055600	Weak transcription	Fetal Heart	heart
45	chr6:57045600-57059400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:57045800-57048800	Strong transcription	HMEC	breast
47	chr6:57045800-57048800	Genic enhancers	HSMM	muscle
48	chr6:57045800-57049000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:57045800-57049400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr6:57045800-57050600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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