Variant report

Variant	rs13212638
Chromosome Location	chr6:38139500-38139501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38138220..38140617-chr6:38142892..38144834,2	K562	blood:
2	chr6:38138513..38140843-chr6:38152378..38154915,2	K562	blood:
3	chr6:38137479..38141029-chr6:38143334..38147856,5	K562	blood:
4	chr6:38137479..38141029-chr6:38144999..38147856,3	K562	blood:
5	chr6:38129827..38133473-chr6:38138909..38141756,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10807190	0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs10807191	0.84[JPT][hapmap]
rs10947714	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947716	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11754110	0.82[GIH][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11756830	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs12196879	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12197001	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12198616	0.89[ASW][hapmap];0.82[CHB][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12206712	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13198420	1.00[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13205068	0.86[JPT][hapmap]
rs2092426	0.91[ASN][1000 genomes]
rs2143403	0.86[JPT][hapmap]
rs2235710	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2235711	0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3800358	0.84[JPT][hapmap]
rs4314486	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6458044	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71556980	0.85[ASN][1000 genomes]
rs735117	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs737171	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs742537	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs742538	0.86[JPT][hapmap]
rs742539	0.94[ASN][1000 genomes]
rs761153	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7742915	0.84[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7756835	0.86[JPT][hapmap]
rs909998	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9380721	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9462400	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9462404	0.85[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470806	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470807	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470811	0.84[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9470813	0.82[GIH][hapmap]
rs9470816	0.86[JPT][hapmap]
rs9470818	0.86[JPT][hapmap]
rs9470819	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470820	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470822	0.92[JPT][hapmap]
rs9470823	0.86[JPT][hapmap]
rs9470825	0.89[CHD][hapmap];0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	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
4	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv524213	chr6:38106844-38160627	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv517973	chr6:38131442-38152460	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13212638	RPL10A	cis	parietal	SCAN
rs13212638	C6orf126	cis	parietal	SCAN
rs13212638	GLO1	cis	parietal	SCAN
rs13212638	ZFAND3	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38091400-38141800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:38121000-38159600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:38121400-38141000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:38121800-38153600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:38123200-38153200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:38123400-38155400	Weak transcription	Aorta	Aorta
7	chr6:38123400-38157000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:38123400-38176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:38123600-38140800	Weak transcription	Placenta	Placenta
10	chr6:38123600-38144200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:38123600-38153000	Weak transcription	Primary B cells from cord blood	blood
12	chr6:38123800-38141400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:38123800-38151200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:38124000-38152200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:38124200-38151800	Weak transcription	Brain Anterior Caudate	brain
16	chr6:38124400-38144200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:38127400-38141000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:38127600-38140600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:38129200-38145600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:38129400-38141200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:38129400-38141200	Weak transcription	Lung	lung
22	chr6:38129400-38144600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:38129600-38141200	Weak transcription	Primary T cells from cord blood	blood
24	chr6:38130000-38144400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:38130200-38140800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:38130600-38141200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:38131200-38143800	Weak transcription	Thymus	Thymus
28	chr6:38131800-38140000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:38131800-38140600	Weak transcription	Left Ventricle	heart
30	chr6:38131800-38167800	Weak transcription	Right Atrium	heart
31	chr6:38132600-38141200	Weak transcription	Ovary	ovary
32	chr6:38133000-38140200	Weak transcription	Stomach Mucosa	stomach
33	chr6:38133600-38141000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:38133600-38144600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:38133600-38160400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:38133600-38164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:38133800-38140400	Weak transcription	Adipose Nuclei	Adipose
38	chr6:38136000-38159800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr6:38136600-38139800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:38136800-38145200	Genic enhancers	Fetal Intestine Small	intestine
41	chr6:38136800-38156000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:38137000-38140200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:38137200-38139800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:38137200-38143000	Enhancers	Fetal Intestine Large	intestine
45	chr6:38137600-38141000	Enhancers	Duodenum Mucosa	Duodenum
46	chr6:38137600-38141400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:38137600-38141400	Weak transcription	Right Ventricle	heart
48	chr6:38137600-38144200	Strong transcription	Spleen	Spleen
49	chr6:38138200-38139600	Enhancers	Fetal Brain Male	brain
50	chr6:38138200-38142200	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links