Variant report

Variant	rs140147
Chromosome Location	chr22:30184599-30184600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30183374..30186087-chr22:30189628..30192258,4	MCF-7	breast:
2	chr22:30127476..30130014-chr22:30183535..30186061,2	MCF-7	breast:
3	chr22:30182549..30186689-chr22:30188373..30192437,4	K562	blood:
4	chr22:30181656..30186213-chr22:30190409..30196916,8	MCF-7	breast:
5	chr22:30183311..30186550-chr22:30186984..30189560,4	MCF-7	breast:
6	chr22:30182549..30185414-chr22:30188242..30189873,2	K562	blood:
7	chr22:30182004..30185271-chr22:30192660..30196046,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1076135	0.85[CEU][hapmap]
rs131262	0.85[CEU][hapmap]
rs131269	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs131274	0.80[AMR][1000 genomes]
rs131289	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs131293	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs131295	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs140095	0.83[AMR][1000 genomes]
rs140118	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs140124	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs140145	0.92[CEU][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs140149	0.92[CEU][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs140150	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17462966	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs17711377	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2057882	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2074706	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2074707	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2079338	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2301402	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs28749829	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3788417	0.85[CHB][hapmap]
rs3958027	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5752964	0.88[CEU][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5752975	0.92[CEU][hapmap]
rs5752978	1.00[CEU][hapmap]
rs5763512	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5997529	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5997530	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5997535	0.87[AMR][1000 genomes]
rs5997549	0.85[AMR][1000 genomes]
rs6006274	0.88[AMR][1000 genomes]
rs6006288	0.85[AMR][1000 genomes]
rs713656	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs713657	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7287434	0.85[AMR][1000 genomes]
rs740041	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9306465	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9306468	1.00[CEU][hapmap]
rs9614077	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs997913	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs140147	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30164600-30185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:30164600-30188600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr22:30166800-30194400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr22:30167200-30187800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr22:30167400-30185400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr22:30175400-30194000	Weak transcription	Hela-S3	cervix
7	chr22:30177000-30189000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:30177200-30186000	Weak transcription	Fetal Kidney	kidney
9	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr22:30178400-30193000	Weak transcription	A549	lung
11	chr22:30178600-30184800	Weak transcription	Colon Smooth Muscle	Colon
12	chr22:30178800-30186000	Weak transcription	K562	blood
13	chr22:30178800-30186000	Weak transcription	NH-A	brain
14	chr22:30179200-30185600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr22:30180200-30186800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr22:30180800-30187800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr22:30181200-30185400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr22:30181200-30188200	Weak transcription	Fetal Brain Male	brain
19	chr22:30181200-30196200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr22:30181200-30196200	Weak transcription	Fetal Heart	heart
21	chr22:30181400-30185400	Weak transcription	NHDF-Ad	bronchial
22	chr22:30181400-30185600	Weak transcription	Psoas Muscle	Psoas
23	chr22:30182000-30194600	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr22:30182200-30194000	Strong transcription	Fetal Muscle Leg	muscle
25	chr22:30182200-30217000	Strong transcription	Fetal Intestine Small	intestine
26	chr22:30182200-30222200	Strong transcription	Thymus	Thymus
27	chr22:30182400-30184800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr22:30182400-30184800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr22:30182400-30185200	Weak transcription	Fetal Lung	lung
30	chr22:30182400-30192800	Strong transcription	Brain Hippocampus Middle	brain
31	chr22:30182600-30194800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr22:30182800-30185800	Genic enhancers	Spleen	Spleen
33	chr22:30182800-30192000	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr22:30182800-30192800	Strong transcription	Fetal Thymus	thymus
35	chr22:30182800-30194400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr22:30182800-30194600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr22:30182800-30194600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr22:30182800-30204600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:30182800-30204800	Strong transcription	Fetal Brain Female	brain
40	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
41	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
42	chr22:30183000-30188600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr22:30183000-30189000	Strong transcription	HUVEC	blood vessel
44	chr22:30183000-30189800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr22:30183000-30191600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr22:30183000-30192600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr22:30183000-30192600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr22:30183000-30192800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr22:30183000-30193000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr22:30183000-30193000	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links