Variant report

Variant	rs10497618
Chromosome Location	chr2:183870146-183870147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183868651..183871768-chr2:183900854..183904260,4	MCF-7	breast:
2	chr2:183851338..183853468-chr2:183869979..183871906,2	MCF-7	breast:
3	chr2:183858969..183864353-chr2:183866249..183870537,6	K562	blood:
4	chr2:183854920..183857735-chr2:183869263..183871227,2	K562	blood:
5	chr2:183858833..183861882-chr2:183868102..183871099,4	K562	blood:
6	chr2:183865248..183868928-chr2:183869372..183873704,5	K562	blood:
7	chr2:183867603..183870699-chr2:183902943..183904613,3	K562	blood:

Variant related genes	Relation type
ENSG00000061676	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10177344	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10187158	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10187800	1.00[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];0.96[ASN][1000 genomes]
rs10221950	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1022337	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs10931052	0.81[ASW][hapmap];0.80[MEX][hapmap]
rs10931053	0.81[ASW][hapmap]
rs10931055	0.83[AFR][1000 genomes]
rs13385317	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13399354	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16823924	0.88[CHB][hapmap]
rs2271671	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2368352	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28429165	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28832369	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35285912	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3791247	0.88[CHB][hapmap]
rs4427983	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4666603	0.87[AFR][1000 genomes]
rs62190103	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62190104	0.87[AFR][1000 genomes]
rs6719673	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7562515	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7566668	0.81[ASW][hapmap];0.80[MEX][hapmap]
rs9288088	0.81[ASW][hapmap]
rs9333279	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9333280	0.81[ASW][hapmap];0.80[MEX][hapmap]
rs9789450	0.81[ASW][hapmap];0.80[MEX][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	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10497618	DUSP19	cis	parietal	SCAN
rs10497618	NCKAP1	cis	parietal	SCAN
rs10497618	FRZB	cis	cerebellum	SCAN
rs10497618	NCKAP1	cis	cerebellum	SCAN
rs10497618	ZNF804A	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
2	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
3	chr2:183805600-183874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:183812200-183874800	Weak transcription	Gastric	stomach
5	chr2:183814600-183874800	Weak transcription	Aorta	Aorta
6	chr2:183814600-183893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:183827200-183874400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:183833600-183874800	Weak transcription	Brain Substantia Nigra	brain
9	chr2:183833600-183874800	Weak transcription	Pancreas	Pancrea
10	chr2:183833600-183878400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:183833600-183879600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:183842400-183874800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:183846000-183902000	Weak transcription	Lung	lung
14	chr2:183852600-183874400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:183853000-183874800	Weak transcription	Brain Angular Gyrus	brain
16	chr2:183853200-183874800	Weak transcription	Right Atrium	heart
17	chr2:183854000-183898800	Weak transcription	Fetal Brain Male	brain
18	chr2:183855600-183874800	Weak transcription	Hela-S3	cervix
19	chr2:183858400-183874800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:183858400-183874800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:183858600-183870400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:183859400-183872400	Weak transcription	Spleen	Spleen
23	chr2:183859600-183870600	Weak transcription	Brain Anterior Caudate	brain
24	chr2:183859600-183882000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:183859600-183899400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:183861000-183874800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:183862400-183894400	Weak transcription	Placenta	Placenta
28	chr2:183863000-183874800	Weak transcription	Ovary	ovary
29	chr2:183864800-183871600	Weak transcription	Left Ventricle	heart
30	chr2:183864800-183874400	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:183865000-183874400	Weak transcription	A549	lung
32	chr2:183865000-183874800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:183865400-183876600	Weak transcription	HMEC	breast
34	chr2:183865800-183874800	Weak transcription	Small Intestine	intestine
35	chr2:183866000-183870600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:183866000-183871600	Weak transcription	Fetal Intestine Small	intestine
37	chr2:183866000-183871800	Weak transcription	Psoas Muscle	Psoas
38	chr2:183866000-183874400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:183866000-183874400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:183866000-183874800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:183866000-183874800	Weak transcription	Fetal Stomach	stomach
42	chr2:183866000-183874800	Weak transcription	NHEK	skin
43	chr2:183866000-183878000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:183866000-183881400	Weak transcription	HUVEC	blood vessel
45	chr2:183866000-183881800	Weak transcription	Brain Germinal Matrix	brain
46	chr2:183866200-183874800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:183866200-183874800	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:183866200-183874800	Weak transcription	HSMMtube	muscle
49	chr2:183866200-183874800	Weak transcription	NHLF	lung
50	chr2:183866200-183881400	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links