Variant report

Variant	rs5763614
Chromosome Location	chr22:30331290-30331291
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	chr22:30330994..30332769-chr22:30343214..30346064,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1076135	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12710565	0.83[EUR][1000 genomes]
rs140118	0.88[YRI][hapmap]
rs140124	0.88[YRI][hapmap]
rs140145	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs140147	1.00[CEU][hapmap]
rs140149	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs1807508	0.81[EUR][1000 genomes]
rs1807513	0.83[EUR][1000 genomes]
rs1894473	1.00[YRI][hapmap]
rs1894474	0.81[ASN][1000 genomes]
rs193474	0.81[AMR][1000 genomes]
rs193476	0.80[AMR][1000 genomes]
rs1989870	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2007446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2007458	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs2074706	0.83[CEU][hapmap]
rs2074707	0.83[CEU][hapmap]
rs2189802	0.83[EUR][1000 genomes]
rs2285667	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301402	0.86[CEU][hapmap]
rs3747149	0.80[EUR][1000 genomes]
rs3788420	0.84[EUR][1000 genomes]
rs3958027	0.82[EUR][1000 genomes]
rs41156	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs41157	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs41159	0.81[EUR][1000 genomes]
rs41161	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41165	0.93[CEU][hapmap]
rs41168	1.00[CEU][hapmap]
rs41170	0.84[AFR][1000 genomes]
rs41171	1.00[CEU][hapmap]
rs41173	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41176	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4823076	0.80[AMR][1000 genomes]
rs5752961	0.84[JPT][hapmap]
rs5752964	0.89[CEU][hapmap]
rs5752973	0.82[EUR][1000 genomes]
rs5752975	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs5752978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752992	0.84[EUR][1000 genomes]
rs5763512	0.83[CEU][hapmap]
rs5763559	0.82[EUR][1000 genomes]
rs5763565	0.82[EUR][1000 genomes]
rs5763581	0.82[EUR][1000 genomes]
rs5763589	0.82[EUR][1000 genomes]
rs5763591	0.85[EUR][1000 genomes]
rs5763592	0.86[AFR][1000 genomes]
rs5763638	0.82[EUR][1000 genomes]
rs5763645	0.82[EUR][1000 genomes]
rs5763649	0.82[EUR][1000 genomes]
rs5763650	0.81[EUR][1000 genomes]
rs5763651	0.81[EUR][1000 genomes]
rs5763670	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763671	0.84[EUR][1000 genomes]
rs5763688	0.82[EUR][1000 genomes]
rs5763775	0.96[CEU][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes]
rs5763779	1.00[CEU][hapmap]
rs59663694	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5997530	0.83[CEU][hapmap]
rs5997546	0.82[EUR][1000 genomes]
rs5997549	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6006288	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6006300	0.84[EUR][1000 genomes]
rs6006315	1.00[YRI][hapmap]
rs713656	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs713657	0.83[CEU][hapmap]
rs7285583	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7287570	0.80[AMR][1000 genomes]
rs7289604	0.89[EUR][1000 genomes]
rs73162764	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737908	0.82[EUR][1000 genomes]
rs737911	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs737939	0.87[EUR][1000 genomes]
rs740041	0.83[CEU][hapmap]
rs9306465	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs9306468	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs960987	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614077	0.82[EUR][1000 genomes]
rs9614100	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9614102	0.81[EUR][1000 genomes]
rs997913	0.93[CEU][hapmap];0.84[EUR][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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1064489	chr22:30316627-30361881	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869764	chr22:30323649-30367813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1058511	chr22:30330447-30361881	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv2763694	chr22:30330459-30361881	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5763614	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30311000-30333200	Weak transcription	Primary B cells from cord blood	blood
2	chr22:30311600-30343800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:30311800-30340400	Weak transcription	HSMM	muscle
4	chr22:30312600-30339800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr22:30313000-30343800	Weak transcription	Fetal Stomach	stomach
6	chr22:30313600-30339800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr22:30313600-30354200	Weak transcription	Small Intestine	intestine
8	chr22:30314200-30334200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr22:30318000-30334000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr22:30319800-30333800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr22:30320400-30333800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr22:30320600-30339800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr22:30321400-30339800	Weak transcription	Lung	lung
14	chr22:30321800-30334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr22:30322000-30332200	Weak transcription	Fetal Intestine Small	intestine
16	chr22:30324400-30337800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr22:30327600-30331800	Weak transcription	Pancreas	Pancrea
18	chr22:30327600-30342200	Weak transcription	Brain Angular Gyrus	brain
19	chr22:30328200-30333800	Weak transcription	Primary T cells from cord blood	blood
20	chr22:30328400-30332000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr22:30328400-30333800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr22:30328400-30343600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr22:30328400-30351800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr22:30328600-30332200	Weak transcription	Adipose Nuclei	Adipose
25	chr22:30328600-30332400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr22:30328800-30333400	Weak transcription	GM12878-XiMat	blood
27	chr22:30329000-30331400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr22:30329000-30332000	Weak transcription	HUVEC	blood vessel
29	chr22:30329200-30331800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr22:30329400-30331400	Enhancers	Brain Substantia Nigra	brain
31	chr22:30329800-30332200	Weak transcription	Brain Anterior Caudate	brain
32	chr22:30330400-30331800	Weak transcription	Left Ventricle	heart
33	chr22:30330400-30331800	Weak transcription	Psoas Muscle	Psoas
34	chr22:30330400-30332000	Weak transcription	Brain Hippocampus Middle	brain
35	chr22:30330400-30333800	Weak transcription	Right Atrium	heart
36	chr22:30330600-30331600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr22:30330600-30331600	Weak transcription	A549	lung
38	chr22:30330600-30339400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr22:30330600-30342200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr22:30331000-30331400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr22:30331000-30331400	Weak transcription	Ovary	ovary
42	chr22:30331200-30331400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr22:30331200-30331800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr22:30331200-30332600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr22:30331200-30332600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr22:30331200-30332800	Enhancers	Stomach Mucosa	stomach
47	chr22:30331200-30334800	Enhancers	Cortex derived primary cultured neurospheres	brain

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