Variant report

Variant	rs10127438
Chromosome Location	chr1:62560928-62560929
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	chr1:62560418..62562159-chr1:62563244..62565670,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11207901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964872	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2025290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4255414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4915796	0.94[CEU][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4915797	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56777178	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58323203	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58585691	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295242	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61777670	0.86[EUR][1000 genomes]
rs61777684	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61777691	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6684468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6688017	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7512777	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531424	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7535670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537716	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10127438	ROR1	cis	cerebellum	SCAN
rs10127438	INADL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
3	chr1:62532600-62568200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:62532600-62569200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:62532600-62587600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:62532800-62569000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:62536800-62566000	Weak transcription	Gastric	stomach
9	chr1:62541600-62563000	Weak transcription	Lung	lung
10	chr1:62542400-62586800	Weak transcription	NHEK	skin
11	chr1:62542400-62587400	Weak transcription	HMEC	breast
12	chr1:62542600-62563000	Weak transcription	Aorta	Aorta
13	chr1:62543400-62569400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:62544000-62575800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:62545000-62574800	Weak transcription	Fetal Kidney	kidney
16	chr1:62545400-62606800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:62548200-62594000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:62550200-62607800	Weak transcription	Right Ventricle	heart
20	chr1:62551400-62576000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:62551800-62594200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:62551800-62614000	Weak transcription	Primary T cells from cord blood	blood
23	chr1:62553000-62579000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:62553000-62582800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:62553200-62594200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:62553400-62579600	Weak transcription	Pancreas	Pancrea
27	chr1:62553600-62563000	Weak transcription	Fetal Intestine Small	intestine
28	chr1:62553600-62579600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:62554200-62562800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:62554200-62614000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:62554400-62565000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:62554400-62581600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:62555000-62589800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:62555000-62594200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:62555200-62563000	Weak transcription	Esophagus	oesophagus
36	chr1:62555600-62561000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:62555600-62563000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:62555600-62563000	Weak transcription	Fetal Intestine Large	intestine
39	chr1:62555600-62569400	Weak transcription	Ovary	ovary
40	chr1:62555800-62569600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:62555800-62571000	Weak transcription	HepG2	liver
42	chr1:62556000-62565400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:62556000-62566600	Weak transcription	Fetal Heart	heart
44	chr1:62556000-62594200	Weak transcription	Left Ventricle	heart
45	chr1:62556600-62561000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:62556600-62569400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:62557000-62561600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:62557000-62562800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:62559000-62566200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:62559600-62582000	Weak transcription	Liver	Liver

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