Variant report

Variant	rs10931279
Chromosome Location	chr2:153619295-153619296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153612625..153615210-chr2:153618975..153622018,4	K562	blood:
2	chr2:153573784..153577602-chr2:153618161..153622533,3	K562	blood:
3	chr2:153559758..153562464-chr2:153616501..153619452,2	K562	blood:
4	chr2:153618496..153621083-chr2:153625320..153627724,2	K562	blood:
5	chr2:153600659..153603319-chr2:153618153..153620356,2	MCF-7	breast:
6	chr2:153618898..153620403-chr2:153623294..153625594,2	K562	blood:

Variant related genes	Relation type
ENSG00000196504	Chromatin interaction
ENSG00000177917	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10497113	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10931263	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10931271	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1135617	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11674911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11676069	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11901227	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12475871	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12989903	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12995388	0.83[EUR][1000 genomes]
rs12999331	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs13003670	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13006652	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13014141	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13017131	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13022436	0.83[EUR][1000 genomes]
rs1370499	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs16831391	1.00[ASW][hapmap]
rs16831456	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs17328776	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17400456	0.83[EUR][1000 genomes]
rs17400938	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17400952	0.88[AMR][1000 genomes]
rs17400980	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2083097	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2346551	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34199006	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34454505	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34619076	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34775858	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35002744	0.81[EUR][1000 genomes]
rs35421285	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35754252	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36107565	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36122595	0.83[EUR][1000 genomes]
rs3811568	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs3811569	0.85[CEU][hapmap]
rs4575677	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6434172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66849546	0.83[EUR][1000 genomes]
rs6728189	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6736003	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs71417235	0.83[EUR][1000 genomes]
rs7591590	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7598878	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv834422	chr2:153589448-153743069	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv875294	chr2:153607506-153733325	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1013092	chr2:153619295-153683760	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10931279	ARL6IP6	cis	brain	BrainEAC

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153575800-153621400	Weak transcription	Pancreas	Pancrea
2	chr2:153587600-153621600	Weak transcription	NHEK	skin
3	chr2:153588600-153619400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:153590400-153620400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:153593200-153628400	Weak transcription	Fetal Kidney	kidney
6	chr2:153593600-153621800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:153593800-153620000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:153593800-153621400	Weak transcription	HMEC	breast
9	chr2:153593800-153621600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:153595200-153621800	Weak transcription	Aorta	Aorta
11	chr2:153595200-153622000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:153595400-153621600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:153596400-153619400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:153596600-153621400	Weak transcription	Ovary	ovary
15	chr2:153596600-153621400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:153597000-153619800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:153597600-153620600	Strong transcription	Dnd41	blood
18	chr2:153600600-153623400	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:153601400-153619600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:153602200-153620600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:153602200-153621200	Weak transcription	Fetal Brain Female	brain
22	chr2:153602400-153620600	Weak transcription	Fetal Brain Male	brain
23	chr2:153606600-153619400	Weak transcription	Fetal Heart	heart
24	chr2:153607600-153619400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr2:153608800-153620600	Strong transcription	Primary B cells from cord blood	blood
26	chr2:153608800-153621200	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:153609400-153621400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:153609400-153621800	Weak transcription	Spleen	Spleen
29	chr2:153609600-153619800	Weak transcription	Fetal Intestine Large	intestine
30	chr2:153611600-153619800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:153611800-153619400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:153611800-153620200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:153612200-153619800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:153612200-153620000	Weak transcription	Lung	lung
35	chr2:153612200-153620200	Weak transcription	Brain Germinal Matrix	brain
36	chr2:153612200-153621800	Weak transcription	Esophagus	oesophagus
37	chr2:153612400-153621000	Weak transcription	Fetal Intestine Small	intestine
38	chr2:153612400-153621800	Weak transcription	Fetal Stomach	stomach
39	chr2:153612800-153620400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:153613200-153619600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:153613400-153620600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:153613800-153621400	Weak transcription	GM12878-XiMat	blood
43	chr2:153613800-153622600	Weak transcription	A549	lung
44	chr2:153614000-153625000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:153614600-153621600	Weak transcription	K562	blood
46	chr2:153614800-153619600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:153615400-153622200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:153615400-153623200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:153615600-153621600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:153615800-153621000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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