Variant report

Variant	rs2857650
Chromosome Location	chr22:30073681-30073682
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	chr22:30072285..30075839-chr22:30076245..30080235,3	MCF-7	breast:
2	chr22:30071846..30074017-chr22:30075750..30077938,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1034880	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1476757	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]
rs2071622	0.98[AFR][1000 genomes]
rs2245185	0.85[JPT][hapmap]
rs2252472	0.86[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2252587	0.86[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2267150	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267151	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283863	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283864	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527337	0.86[JPT][hapmap]
rs2530667	0.80[ASN][1000 genomes]
rs2530668	0.86[JPT][hapmap]
rs2530670	0.85[JPT][hapmap]
rs2530672	0.86[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2530673	0.86[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2530675	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2530676	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2531850	0.86[JPT][hapmap]
rs2857639	0.85[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes]
rs2857640	0.86[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2857641	0.85[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes]
rs2857642	0.85[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2857645	0.88[YRI][hapmap];0.93[AFR][1000 genomes]
rs2857648	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857649	0.97[EUR][1000 genomes]
rs2857651	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763409	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5763422	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763423	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763431	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7291645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs737931	1.00[CEU][hapmap];0.94[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];0.94[ASN][1000 genomes]
rs9608806	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2857650	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
3	chr22:30050200-30075000	Strong transcription	Stomach Smooth Muscle	stomach
4	chr22:30050200-30084800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr22:30050400-30084400	Strong transcription	Left Ventricle	heart
6	chr22:30050400-30093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr22:30050800-30084800	Strong transcription	Thymus	Thymus
8	chr22:30051000-30083600	Strong transcription	Fetal Muscle Leg	muscle
9	chr22:30051000-30085400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr22:30051400-30082600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr22:30053400-30084400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr22:30053400-30087400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr22:30053800-30081000	Strong transcription	Fetal Intestine Large	intestine
14	chr22:30053800-30084600	Strong transcription	Fetal Stomach	stomach
15	chr22:30054000-30094800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr22:30055400-30095200	Strong transcription	Fetal Intestine Small	intestine
17	chr22:30056000-30094800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr22:30056200-30084600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr22:30056200-30084800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr22:30056400-30084600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr22:30057800-30085600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr22:30057800-30086000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr22:30058200-30084200	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr22:30059600-30081800	Strong transcription	NHLF	lung
25	chr22:30060000-30084800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr22:30060200-30093600	Strong transcription	Fetal Thymus	thymus
27	chr22:30060600-30081600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr22:30061000-30074600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr22:30061000-30083600	Strong transcription	NH-A	brain
30	chr22:30061000-30084400	Strong transcription	Osteobl	bone
31	chr22:30062000-30084600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr22:30062400-30078200	Strong transcription	Adipose Nuclei	Adipose
33	chr22:30063000-30080000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr22:30063000-30080400	Strong transcription	NHDF-Ad	bronchial
35	chr22:30063000-30081200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr22:30063000-30083400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr22:30063200-30084000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr22:30063200-30084400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr22:30063200-30084400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr22:30063200-30084600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr22:30063400-30075400	Strong transcription	Aorta	Aorta
42	chr22:30063400-30081200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr22:30063400-30084400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr22:30063400-30084400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr22:30063400-30084600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr22:30063400-30084800	Strong transcription	Dnd41	blood
47	chr22:30063400-30085000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr22:30063400-30094600	Strong transcription	Primary T cells from cord blood	blood
49	chr22:30063600-30075600	Strong transcription	Placenta	Placenta
50	chr22:30063600-30084600	Strong transcription	Liver	Liver

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