Variant report

Variant	rs10948238
Chromosome Location	chr6:45511541-45511542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45510384..45512325-chr6:45518225..45520271,2	MCF-7	breast:
2	chr6:45507057..45510160-chr6:45510920..45514635,4	MCF-7	breast:
3	chr6:45507659..45510027-chr6:45511136..45513669,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10214519	1.00[JPT][hapmap]
rs10485422	0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10948236	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10948237	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756145	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1200428	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12195878	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12197948	1.00[JPT][hapmap]
rs12204049	0.83[ASN][1000 genomes]
rs12209785	0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12210100	1.00[JPT][hapmap]
rs1316330	1.00[JPT][hapmap]
rs1317777	1.00[JPT][hapmap]
rs13201287	0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13207392	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1928533	0.87[ASW][hapmap];0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1934327	1.00[JPT][hapmap]
rs1934329	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031966	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2396442	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2677110	1.00[JPT][hapmap]
rs2790098	1.00[JPT][hapmap]
rs2819864	1.00[JPT][hapmap]
rs2819866	1.00[JPT][hapmap]
rs4438954	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4714854	1.00[JPT][hapmap]
rs6458445	0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6458446	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6458447	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904353	0.87[ASW][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905181	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6905847	0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6911664	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6915569	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864634	0.83[ASN][1000 genomes]
rs7748231	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755257	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7756094	1.00[ASN][1000 genomes]
rs7760160	1.00[ASN][1000 genomes]
rs7772562	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9472494	1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1019561	chr6:45485826-45535222	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv538214	chr6:45485826-45535222	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv491939	chr6:45508319-45526327	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10948238	RPL7L1	cis	cerebellum	SCAN
rs10948238	HSP90AB1	cis	parietal	SCAN
rs10948238	KLHDC3	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45465000-45521600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr6:45481400-45514600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:45482800-45514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:45484400-45514600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:45489000-45521800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:45493200-45516200	Weak transcription	Hela-S3	cervix
7	chr6:45498600-45514600	Weak transcription	Dnd41	blood
8	chr6:45500200-45513800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:45500600-45514600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:45500600-45516600	Weak transcription	Small Intestine	intestine
11	chr6:45502000-45516200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:45503000-45514600	Weak transcription	Esophagus	oesophagus
13	chr6:45504200-45514600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:45504600-45513200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:45505400-45512200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:45506000-45514400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:45506000-45514600	Weak transcription	Pancreas	Pancrea
18	chr6:45506800-45514600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:45506800-45514600	Weak transcription	Gastric	stomach
20	chr6:45506800-45523400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:45507400-45518800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:45508200-45517200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:45508200-45521600	Weak transcription	Primary T cells from cord blood	blood
24	chr6:45508200-45530600	Weak transcription	Psoas Muscle	Psoas
25	chr6:45508600-45514600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:45508600-45514600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:45508600-45522400	Weak transcription	Fetal Thymus	thymus
28	chr6:45508800-45516600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:45508800-45523400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:45509200-45512600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr6:45509400-45512000	Enhancers	NHDF-Ad	bronchial
32	chr6:45509600-45512000	Enhancers	Fetal Heart	heart
33	chr6:45509600-45512000	Genic enhancers	HSMM	muscle
34	chr6:45509600-45512000	Enhancers	Osteobl	bone
35	chr6:45509600-45512200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:45509800-45511600	Enhancers	NHLF	lung
37	chr6:45509800-45512000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr6:45509800-45512400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:45509800-45512800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:45509800-45514600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr6:45510000-45512000	Enhancers	HSMMtube	muscle
42	chr6:45510000-45513800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr6:45510200-45514600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:45510600-45512000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:45510600-45512000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:45510800-45511600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:45510800-45512400	Enhancers	HMEC	breast
48	chr6:45510800-45514200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:45511000-45511800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:45511000-45512000	Enhancers	NHEK	skin

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