Variant report

Variant	rs10961628
Chromosome Location	chr9:14633286-14633287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10756587	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10756590	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10810185	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10810192	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10810193	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10810195	0.87[ASN][1000 genomes]
rs10961601	0.82[CHB][hapmap]
rs10961617	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10961622	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10961625	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10961626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10961627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10961630	0.99[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1130072	0.81[CEU][hapmap]
rs1134457	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1143025	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11536695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236525	0.82[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13290060	0.93[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13290946	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1343568	0.81[CEU][hapmap]
rs1343706	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1410303	0.82[AMR][1000 genomes]
rs2225163	0.82[CHB][hapmap]
rs2382489	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2382492	0.93[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765603	0.84[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3819003	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4265280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460485	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4490946	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4741409	0.83[ASN][1000 genomes]
rs7027971	0.88[ASN][1000 genomes]
rs7032825	0.82[CHB][hapmap]
rs7036226	0.90[ASN][1000 genomes]
rs7873022	0.93[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv831517	chr9:14512924-14738206	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv521363	chr9:14566406-14691897	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv892605	chr9:14585052-14709151	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv892606	chr9:14588049-14697022	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892608	chr9:14589173-14689088	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv892609	chr9:14589173-14694302	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv613642	chr9:14592180-14639666	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv2752921	chr9:14593749-14694372	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv2755661	chr9:14615367-14660700	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv892610	chr9:14622952-14654900	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv3450970	chr9:14631802-14633750	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10961628	ZDHHC21	Cis_1M	lymphoblastoid	RTeQTL
rs10961628	ZDHHC21	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14594800-14633400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr9:14595600-14653600	Weak transcription	NHDF-Ad	bronchial
3	chr9:14596600-14634000	Weak transcription	Gastric	stomach
4	chr9:14596600-14653600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:14597000-14655000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:14597800-14633600	Weak transcription	Pancreas	Pancrea
7	chr9:14599800-14654000	Weak transcription	Fetal Heart	heart
8	chr9:14601400-14636800	Weak transcription	Small Intestine	intestine
9	chr9:14605600-14654800	Weak transcription	HSMM	muscle
10	chr9:14605800-14634000	Weak transcription	Esophagus	oesophagus
11	chr9:14610200-14654800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:14612800-14641200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:14613600-14654600	Weak transcription	Fetal Kidney	kidney
14	chr9:14617200-14634000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:14617200-14646000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:14617400-14634200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr9:14619400-14653600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:14619400-14654800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:14619600-14654800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:14626400-14638600	Weak transcription	HUVEC	blood vessel
21	chr9:14626800-14655000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:14627800-14643400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:14628000-14639400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:14628000-14640800	Weak transcription	Colon Smooth Muscle	Colon
25	chr9:14629200-14634000	Weak transcription	Dnd41	blood
26	chr9:14629200-14636400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr9:14629400-14635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:14629400-14637600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr9:14629400-14654600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:14629400-14655000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:14629800-14633600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:14630000-14633400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:14630000-14654400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr9:14630200-14637400	Strong transcription	Primary B cells from cord blood	blood
35	chr9:14630400-14654800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr9:14630600-14633400	Strong transcription	Fetal Lung	lung
37	chr9:14630600-14635600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:14631000-14654000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:14631000-14654800	Weak transcription	Brain Anterior Caudate	brain
40	chr9:14631000-14654800	Weak transcription	Brain Hippocampus Middle	brain
41	chr9:14631000-14692400	Weak transcription	HSMMtube	muscle
42	chr9:14631200-14633800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:14631200-14636400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:14631200-14636800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:14631200-14637800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr9:14631200-14638200	Weak transcription	Fetal Brain Male	brain
47	chr9:14631200-14638600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:14631200-14641200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr9:14631200-14653600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr9:14631200-14653600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links