Variant report

Variant	rs41173
Chromosome Location	chr22:30424863-30424864
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30422072..30424953-chr22:30431511..30433741,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1076135	0.83[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1468176	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1548389	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1807508	0.82[EUR][1000 genomes]
rs193471	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs193474	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs193475	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs193476	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1989870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2007446	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2007458	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2285667	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2301402	0.86[CEU][hapmap]
rs2412970	0.81[JPT][hapmap]
rs2412972	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2412976	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3788420	0.81[EUR][1000 genomes]
rs41156	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41157	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41159	0.84[EUR][1000 genomes]
rs41161	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41165	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs41168	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41170	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41176	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4336042	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4820827	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4823076	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5752975	0.93[CEU][hapmap]
rs5752978	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs5752992	0.81[EUR][1000 genomes]
rs5753008	0.80[AMR][1000 genomes]
rs5753025	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5763614	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5763670	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763671	0.81[EUR][1000 genomes]
rs5763688	0.83[EUR][1000 genomes]
rs5763751	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5763775	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5763779	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs5763842	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59663694	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5997579	0.81[JPT][hapmap]
rs7285583	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7287570	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73162764	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs737908	0.81[EUR][1000 genomes]
rs737911	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs757024	0.81[JPT][hapmap]
rs9306468	1.00[CEU][hapmap]
rs960987	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs997913	0.93[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41173	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr22:30392600-30425000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr22:30394800-30425200	Strong transcription	Fetal Intestine Large	intestine
7	chr22:30394800-30426200	Strong transcription	Placenta	Placenta
8	chr22:30396800-30426200	Strong transcription	Primary B cells from cord blood	blood
9	chr22:30397800-30425400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr22:30398000-30426200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr22:30398400-30425000	Strong transcription	Primary hematopoietic stem cells	blood
12	chr22:30398600-30425200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr22:30401600-30425200	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr22:30402200-30425200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr22:30402600-30426200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr22:30402800-30425800	Strong transcription	Fetal Muscle Leg	muscle
17	chr22:30403000-30425200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr22:30404400-30426400	Strong transcription	Primary T cells from cord blood	blood
19	chr22:30404800-30426000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:30406000-30426600	Strong transcription	Thymus	Thymus
21	chr22:30406200-30425200	Strong transcription	Fetal Thymus	thymus
22	chr22:30407800-30425200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr22:30408000-30425800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr22:30408200-30425000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr22:30408400-30425800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr22:30409000-30432800	Strong transcription	Fetal Stomach	stomach
27	chr22:30412000-30431200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr22:30413600-30425600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr22:30414200-30425200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:30415000-30425200	Strong transcription	NHLF	lung
31	chr22:30415000-30425800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr22:30415200-30425000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr22:30415800-30425200	Strong transcription	Fetal Lung	lung
34	chr22:30416400-30427200	Weak transcription	K562	blood
35	chr22:30418400-30425200	Strong transcription	HSMMtube	muscle
36	chr22:30418800-30425600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr22:30419600-30425400	Strong transcription	Osteobl	bone
38	chr22:30419600-30426000	Strong transcription	HSMM	muscle
39	chr22:30419600-30434400	Weak transcription	Small Intestine	intestine
40	chr22:30419800-30425200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr22:30419800-30425200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr22:30419800-30425200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr22:30419800-30427200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr22:30420400-30425400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr22:30420600-30425200	Genic enhancers	Esophagus	oesophagus
46	chr22:30420600-30425200	Strong transcription	Dnd41	blood
47	chr22:30421400-30426200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr22:30422200-30429000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr22:30422400-30425800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr22:30422400-30426400	Genic enhancers	Cortex derived primary cultured neurospheres	brain

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