Variant report

Variant	rs1476757
Chromosome Location	chr22:30088183-30088184
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	chr22:30086550..30091376-chr22:30091742..30099600,10	MCF-7	breast:
2	chr22:30086357..30088684-chr22:30160929..30163029,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100319	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1034880	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071622	0.93[AFR][1000 genomes]
rs2245185	0.85[JPT][hapmap]
rs2252472	0.86[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs2252587	0.86[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs2267150	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2267151	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283863	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283864	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527337	0.86[JPT][hapmap]
rs2530668	0.86[JPT][hapmap]
rs2530670	0.85[JPT][hapmap]
rs2530672	0.86[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs2530673	0.86[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs2530675	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2530676	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2531850	0.86[JPT][hapmap]
rs2857639	0.85[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes]
rs2857640	0.86[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2857641	0.85[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes]
rs2857642	0.85[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2857645	0.88[YRI][hapmap];0.93[AFR][1000 genomes]
rs2857648	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2857649	0.94[EUR][1000 genomes]
rs2857650	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857651	0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752953	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763409	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763422	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763423	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5763431	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7291645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737931	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9608806	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv529737	chr22:30060946-30109561	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv914963	chr22:30075052-30133579	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv914965	chr22:30086144-30112226	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1476757	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
2	chr22:30050400-30093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr22:30054000-30094800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr22:30055400-30095200	Strong transcription	Fetal Intestine Small	intestine
5	chr22:30056000-30094800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr22:30060200-30093600	Strong transcription	Fetal Thymus	thymus
7	chr22:30063400-30094600	Strong transcription	Primary T cells from cord blood	blood
8	chr22:30072800-30088200	Weak transcription	Right Atrium	heart
9	chr22:30075400-30097400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr22:30076800-30096400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr22:30077800-30096400	Weak transcription	Small Intestine	intestine
12	chr22:30079600-30097000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr22:30079600-30097400	Weak transcription	Hela-S3	cervix
14	chr22:30080000-30097000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr22:30080200-30089600	Weak transcription	Colonic Mucosa	Colon
16	chr22:30080200-30098800	Weak transcription	GM12878-XiMat	blood
17	chr22:30081000-30096400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr22:30081200-30096400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr22:30081400-30089000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr22:30082000-30088800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr22:30083200-30090000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr22:30083400-30089000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr22:30083800-30088200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr22:30083800-30088200	Weak transcription	Ovary	ovary
25	chr22:30083800-30088400	Weak transcription	Primary B cells from cord blood	blood
26	chr22:30083800-30088400	Weak transcription	Fetal Intestine Large	intestine
27	chr22:30084000-30089400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr22:30084000-30090000	Weak transcription	Aorta	Aorta
29	chr22:30084200-30088800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr22:30084400-30088600	Weak transcription	Left Ventricle	heart
31	chr22:30084400-30089000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr22:30084400-30089000	Weak transcription	HUVEC	blood vessel
33	chr22:30084400-30089600	Weak transcription	HMEC	breast
34	chr22:30084400-30090400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr22:30084600-30088600	Weak transcription	Gastric	stomach
36	chr22:30084600-30089000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr22:30084600-30089800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr22:30085000-30089000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr22:30085200-30088200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr22:30085200-30088400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr22:30085200-30088400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr22:30085200-30088400	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr22:30085200-30088800	Strong transcription	NHEK	skin
44	chr22:30085600-30088400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr22:30085600-30092000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr22:30085600-30094000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr22:30085800-30089000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:30085800-30089200	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr22:30085800-30089200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr22:30085800-30095000	Strong transcription	Dnd41	blood

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