Variant report

Variant	rs13205068
Chromosome Location	chr6:38162180-38162181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38147181..38149521-chr6:38161439..38163786,2	K562	blood:
2	chr6:38116607..38119118-chr6:38160290..38163067,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10807190	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10807191	0.84[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10807192	0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs10947714	0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10947716	0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11754110	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11756830	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12196879	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12197001	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12198616	0.82[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs12206712	0.81[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13212638	0.86[JPT][hapmap]
rs17678747	0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs17678833	0.89[ASN][1000 genomes]
rs2143403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235710	0.96[ASN][1000 genomes]
rs2235711	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3800358	0.80[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs3823431	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4314486	0.96[ASN][1000 genomes]
rs4510661	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs6458044	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6938410	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs735117	0.81[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs737171	0.86[ASN][1000 genomes]
rs742537	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs742538	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs761153	0.86[JPT][hapmap]
rs7742915	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7756835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909998	0.81[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs926565	0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9380721	0.96[ASN][1000 genomes]
rs9462400	0.94[ASN][1000 genomes]
rs9462404	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9462405	0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9462406	0.85[ASN][1000 genomes]
rs9462409	0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9470807	0.83[JPT][hapmap]
rs9470811	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9470813	0.84[ASW][hapmap];0.89[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9470816	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470818	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470819	0.94[ASN][1000 genomes]
rs9470820	0.94[ASN][1000 genomes]
rs9470822	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470823	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470824	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470825	0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.95[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	nsv885819	chr6:38148770-38190439	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13205068	ZFAND3	cis	cerebellum	SCAN
rs13205068	KCTD20	cis	parietal	SCAN
rs13205068	GLO1	cis	parietal	SCAN
rs13205068	TRERF1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38123400-38176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:38131800-38167800	Weak transcription	Right Atrium	heart
3	chr6:38133600-38164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:38138600-38169400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:38141600-38166200	Weak transcription	Left Ventricle	heart
6	chr6:38141800-38168000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:38143600-38162400	Weak transcription	Right Ventricle	heart
8	chr6:38143600-38177200	Weak transcription	Ovary	ovary
9	chr6:38145200-38163400	Weak transcription	Colonic Mucosa	Colon
10	chr6:38146000-38162400	Weak transcription	Pancreas	Pancrea
11	chr6:38146400-38162400	Weak transcription	Gastric	stomach
12	chr6:38146600-38162400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:38147400-38180400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:38148200-38162200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:38152000-38166600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:38153800-38164400	Weak transcription	Primary B cells from cord blood	blood
17	chr6:38155600-38177200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:38155800-38162800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:38156000-38162400	Weak transcription	Aorta	Aorta
20	chr6:38156000-38162800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:38157800-38166200	Weak transcription	Psoas Muscle	Psoas
22	chr6:38158200-38163200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:38158800-38162400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:38159200-38162200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:38159200-38162600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:38159200-38162600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:38159600-38162800	Strong transcription	Primary T cells from cord blood	blood
28	chr6:38160000-38164000	Weak transcription	Fetal Intestine Small	intestine
29	chr6:38160000-38166000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:38160200-38177600	Weak transcription	Esophagus	oesophagus
31	chr6:38160400-38162200	Enhancers	HUVEC	blood vessel
32	chr6:38160400-38177000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:38160400-38177600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:38160600-38162600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:38160600-38165000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr6:38160600-38177000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:38160600-38179600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:38160800-38201400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:38161000-38162600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:38161000-38162600	Enhancers	Brain Anterior Caudate	brain
41	chr6:38161000-38162600	Enhancers	Lung	lung
42	chr6:38161000-38162800	Enhancers	Fetal Muscle Trunk	muscle
43	chr6:38161000-38163200	Enhancers	Brain Germinal Matrix	brain
44	chr6:38161200-38162600	Enhancers	Fetal Muscle Leg	muscle
45	chr6:38161200-38167400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:38161400-38162400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:38161600-38162600	Weak transcription	Brain Hippocampus Middle	brain
48	chr6:38161600-38162600	Weak transcription	Fetal Brain Female	brain
49	chr6:38161600-38162600	Enhancers	HSMM	muscle
50	chr6:38161600-38163000	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links