Variant report

Variant	rs12202202
Chromosome Location	chr6:38204303-38204304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10456461	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10456462	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10947715	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10947717	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10947719	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11544072	1.00[ASN][1000 genomes]
rs11751094	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11751153	1.00[CHB][hapmap]
rs11751937	1.00[ASN][1000 genomes]
rs11753391	1.00[ASN][1000 genomes]
rs11753408	1.00[ASN][1000 genomes]
rs11753437	1.00[ASN][1000 genomes]
rs11753563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11753759	1.00[ASN][1000 genomes]
rs11754816	1.00[ASN][1000 genomes]
rs11755439	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11755600	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11755721	1.00[ASN][1000 genomes]
rs11756301	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11756626	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11757654	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11757980	1.00[ASN][1000 genomes]
rs11759816	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11760121	1.00[ASN][1000 genomes]
rs11967006	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12201418	1.00[CEU][hapmap]
rs12202872	1.00[ASN][1000 genomes]
rs12212820	0.94[CEU][hapmap]
rs12215376	0.94[EUR][1000 genomes]
rs17757975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1923280	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1931760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4336442	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55707043	1.00[ASN][1000 genomes]
rs55731063	1.00[ASN][1000 genomes]
rs55743233	1.00[ASN][1000 genomes]
rs55786741	1.00[ASN][1000 genomes]
rs55825770	1.00[ASN][1000 genomes]
rs55836194	1.00[ASN][1000 genomes]
rs55878533	1.00[ASN][1000 genomes]
rs55902626	1.00[ASN][1000 genomes]
rs55972258	1.00[ASN][1000 genomes]
rs55990078	1.00[ASN][1000 genomes]
rs56020526	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56021282	1.00[ASN][1000 genomes]
rs56030069	1.00[ASN][1000 genomes]
rs56064162	0.94[EUR][1000 genomes]
rs56178553	1.00[ASN][1000 genomes]
rs56206533	1.00[ASN][1000 genomes]
rs56229452	1.00[ASN][1000 genomes]
rs56308246	1.00[ASN][1000 genomes]
rs56341927	1.00[ASN][1000 genomes]
rs56413211	1.00[ASN][1000 genomes]
rs57564251	1.00[ASN][1000 genomes]
rs58003999	1.00[ASN][1000 genomes]
rs58418493	1.00[ASN][1000 genomes]
rs59693994	1.00[ASN][1000 genomes]
rs60109083	1.00[ASN][1000 genomes]
rs72849815	0.96[EUR][1000 genomes]
rs72849820	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72849852	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72851423	1.00[ASN][1000 genomes]
rs72851457	1.00[ASN][1000 genomes]
rs73419907	1.00[ASN][1000 genomes]
rs73419916	1.00[ASN][1000 genomes]
rs73419919	1.00[ASN][1000 genomes]
rs73419938	1.00[ASN][1000 genomes]
rs73419941	1.00[ASN][1000 genomes]
rs73419944	1.00[ASN][1000 genomes]
rs73419945	1.00[ASN][1000 genomes]
rs73419946	1.00[ASN][1000 genomes]
rs73419947	1.00[ASN][1000 genomes]
rs73419949	1.00[ASN][1000 genomes]
rs73419959	1.00[ASN][1000 genomes]
rs73419960	1.00[ASN][1000 genomes]
rs73419963	1.00[ASN][1000 genomes]
rs73419971	1.00[ASN][1000 genomes]
rs73421810	1.00[ASN][1000 genomes]
rs73421817	1.00[ASN][1000 genomes]
rs73421819	1.00[ASN][1000 genomes]
rs73421822	1.00[ASN][1000 genomes]
rs73421825	1.00[ASN][1000 genomes]
rs73421831	1.00[ASN][1000 genomes]
rs73421842	1.00[ASN][1000 genomes]
rs73421855	1.00[ASN][1000 genomes]
rs73421866	1.00[ASN][1000 genomes]
rs73421874	1.00[ASN][1000 genomes]
rs73421889	1.00[ASN][1000 genomes]
rs73421902	1.00[ASN][1000 genomes]
rs73423525	1.00[ASN][1000 genomes]
rs7739762	1.00[CEU][hapmap]
rs9369034	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9462399	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9462403	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9462434	1.00[ASN][1000 genomes]
rs9470765	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9470779	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS 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	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv520053	chr6:38154941-38207636	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12202202	C6orf126	cis	cerebellum	SCAN
rs12202202	PRICKLE4	cis	parietal	SCAN
rs12202202	SLC26A8	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38167000-38210400	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38178000-38221600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:38178000-38221800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:38181000-38207600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:38181400-38229400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:38186600-38215200	Weak transcription	Aorta	Aorta
7	chr6:38194400-38230200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:38195800-38204400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:38198000-38204600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:38200000-38207600	Weak transcription	Lung	lung
11	chr6:38200600-38204800	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:38200600-38205200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:38200600-38205200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr6:38200600-38205400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:38201000-38204400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:38201600-38207200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:38202200-38207400	Weak transcription	Stomach Mucosa	stomach
18	chr6:38202200-38207600	Weak transcription	Gastric	stomach
19	chr6:38203200-38204400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:38203200-38205400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:38203200-38205400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:38203400-38207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:38203400-38212800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:38203800-38205200	Enhancers	GM12878-XiMat	blood
25	chr6:38203800-38207600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:38203800-38207800	Weak transcription	Psoas Muscle	Psoas
27	chr6:38203800-38207800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:38203800-38208000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:38204000-38204400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:38204000-38207800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:38204000-38208800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:38204200-38215200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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