Variant report

Variant	rs7717955
Chromosome Location	chr5:35862841-35862842
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	chr5:35859166..35861325-chr5:35861673..35863431,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10063294	0.82[CHB][hapmap]
rs10213865	1.00[CEU][hapmap];0.93[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10214237	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10214273	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10472984	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11567694	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11567705	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11742240	0.84[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11742270	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12153578	1.00[YRI][hapmap]
rs13188960	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494564	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34463936	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4594881	0.88[AMR][1000 genomes]
rs62351974	0.81[EUR][1000 genomes]
rs62351975	0.82[EUR][1000 genomes]
rs6871748	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6881270	0.84[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6881706	0.84[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6890853	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6897932	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs700172	0.87[YRI][hapmap]
rs7709291	0.85[JPT][hapmap]
rs860413	0.83[MEX][hapmap];0.87[YRI][hapmap]
rs987106	0.82[CHB][hapmap]

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	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv880610	chr5:35850693-35866265	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv880517	chr5:35850693-35870814	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv597813	chr5:35855264-35864590	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv880591	chr5:35859863-35870588	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7717955	LMBRD2	cis	parietal	SCAN
rs7717955	TOMM7	cis	cerebellum	SCAN
rs7717955	DNAJC21	cis	cerebellum	SCAN
rs7717955	C5orf33	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35857400-35869200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
2	chr5:35857800-35866600	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr5:35858200-35863200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:35858200-35864800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:35858800-35864800	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:35858800-35865000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:35858800-35865400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:35858800-35866600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
9	chr5:35859000-35864800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
10	chr5:35859000-35864800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
11	chr5:35859000-35865000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
12	chr5:35859800-35863000	Weak transcription	Lung	lung
13	chr5:35860000-35869000	Weak transcription	HMEC	breast
14	chr5:35860000-35876600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:35860400-35872800	Weak transcription	Spleen	Spleen
16	chr5:35860400-35883800	Weak transcription	Small Intestine	intestine
17	chr5:35860600-35864800	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
18	chr5:35860800-35863800	Weak transcription	Primary B cells from cord blood	blood
19	chr5:35860800-35864800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
20	chr5:35860800-35865000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
21	chr5:35861000-35863800	Transcr. at gene 5' and 3'	Thymus	Thymus
22	chr5:35861200-35863200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:35861200-35863200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:35861200-35870400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:35861600-35863400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:35861600-35863400	Enhancers	NHEK	skin
27	chr5:35862000-35864200	Strong transcription	NHLF	lung
28	chr5:35862200-35863200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr5:35862400-35863800	Enhancers	GM12878-XiMat	blood
30	chr5:35862400-35864400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr5:35862400-35865200	Weak transcription	NH-A	brain
32	chr5:35862400-35870400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr5:35862600-35863400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:35862600-35863400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:35862600-35863400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:35862600-35863800	Strong transcription	HSMM	muscle
37	chr5:35862600-35864600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:35862600-35868200	Strong transcription	Fetal Thymus	thymus
39	chr5:35862600-35868600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:35862600-35876200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:35862800-35863400	Weak transcription	NHDF-Ad	bronchial
42	chr5:35862800-35863600	Weak transcription	Osteobl	bone

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