Variant report

Variant	rs6438068
Chromosome Location	chr3:112056934-112056935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11714917	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs11716857	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs13073116	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17513726	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2280462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399411	0.91[ASN][1000 genomes]
rs2399420	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4234416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4550804	0.91[ASN][1000 genomes]
rs56037521	0.91[ASN][1000 genomes]
rs62264134	0.91[ASN][1000 genomes]
rs62264135	0.91[ASN][1000 genomes]
rs62264136	0.91[ASN][1000 genomes]
rs62264137	0.91[ASN][1000 genomes]
rs6438066	0.83[ASN][1000 genomes]
rs6438067	0.87[ASN][1000 genomes]
rs6771014	0.91[ASN][1000 genomes]
rs6774405	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939576	0.91[ASN][1000 genomes]
rs939577	0.91[ASN][1000 genomes]
rs939578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9814088	0.91[ASN][1000 genomes]
rs9818526	0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6438068	SLC9A10	cis	cerebellum	SCAN
rs6438068	ATP6V1A	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112052600-112062400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:112052600-112066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:112052800-112076200	Weak transcription	Right Ventricle	heart
4	chr3:112053000-112057200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:112053200-112062200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:112053200-112066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:112053200-112076400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:112053400-112057200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:112053400-112057600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:112053800-112057000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:112053800-112057000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:112053800-112063800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:112053800-112064200	Weak transcription	Fetal Intestine Large	intestine
14	chr3:112054000-112057200	Enhancers	Adipose Nuclei	Adipose
15	chr3:112054000-112065800	Weak transcription	Fetal Kidney	kidney
16	chr3:112054000-112068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:112054200-112063800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:112054200-112064000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:112054400-112058800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:112054400-112059200	Weak transcription	Brain Substantia Nigra	brain
21	chr3:112054600-112057000	Enhancers	Brain Anterior Caudate	brain
22	chr3:112054600-112059600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:112054600-112059600	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:112054800-112057000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:112054800-112058000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:112054800-112059400	Weak transcription	Right Atrium	heart
27	chr3:112054800-112059600	Weak transcription	Primary B cells from cord blood	blood
28	chr3:112054800-112060800	Enhancers	Brain Angular Gyrus	brain
29	chr3:112054800-112061800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:112054800-112063400	Weak transcription	Ovary	ovary
31	chr3:112054800-112063800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:112054800-112066400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:112054800-112076800	Weak transcription	Lung	lung
34	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:112055000-112057000	Active TSS	GM12878-XiMat	blood
36	chr3:112055000-112057800	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr3:112055000-112059400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:112055000-112063400	Weak transcription	Brain Germinal Matrix	brain
39	chr3:112055200-112068800	Weak transcription	Fetal Intestine Small	intestine
40	chr3:112055400-112057000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:112055400-112059600	Weak transcription	Fetal Thymus	thymus
42	chr3:112055400-112062200	Weak transcription	Fetal Lung	lung
43	chr3:112055400-112063800	Weak transcription	Fetal Stomach	stomach
44	chr3:112055600-112057200	Weak transcription	Primary T cells from cord blood	blood
45	chr3:112055600-112057800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
46	chr3:112055600-112059000	Weak transcription	Placenta	Placenta
47	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr3:112055800-112076400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:112056000-112057000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:112056000-112057800	Enhancers	Fetal Brain Male	brain

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