Variant report

Variant	rs873935
Chromosome Location	chr12:47627753-47627754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11183779	1.00[CHB][hapmap]
rs11183783	1.00[CHB][hapmap]
rs11183795	1.00[CHB][hapmap]
rs12370622	1.00[CHB][hapmap]
rs1554693	1.00[CHB][hapmap]
rs17821774	1.00[CHB][hapmap]
rs2111903	1.00[CHB][hapmap]
rs214660	0.80[ASN][1000 genomes]
rs214661	0.80[ASN][1000 genomes]
rs2408718	1.00[CHB][hapmap]
rs4768782	1.00[CHB][hapmap]
rs712100	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs7974410	1.00[CHB][hapmap]
rs855141	0.80[ASN][1000 genomes]
rs855142	0.80[ASN][1000 genomes]
rs855144	0.80[ASN][1000 genomes]
rs855145	0.80[ASN][1000 genomes]
rs855146	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs855147	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs855149	0.80[ASN][1000 genomes]
rs855151	0.80[ASN][1000 genomes]
rs855153	0.80[ASN][1000 genomes]
rs855154	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs873935	DNAJC22	cis	cerebellum	SCAN
rs873935	LOC255411	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47583200-47628600	Weak transcription	Aorta	Aorta
2	chr12:47601800-47628400	Weak transcription	Esophagus	oesophagus
3	chr12:47610400-47628400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:47612400-47628400	Weak transcription	Placenta	Placenta
5	chr12:47617200-47628400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:47617200-47628400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:47617200-47629000	Weak transcription	NHEK	skin
8	chr12:47617800-47628400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:47617800-47628400	Weak transcription	Spleen	Spleen
10	chr12:47617800-47629400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:47617800-47631600	Weak transcription	Small Intestine	intestine
12	chr12:47617800-47632800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:47618000-47627800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:47618000-47628400	Weak transcription	HMEC	breast
15	chr12:47618000-47629000	Weak transcription	Adipose Nuclei	Adipose
16	chr12:47618000-47629400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:47618600-47630000	Weak transcription	HSMM	muscle
18	chr12:47618600-47638600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:47619000-47628400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:47619000-47632800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:47619000-47643600	Weak transcription	Pancreas	Pancrea
22	chr12:47620200-47630200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:47620200-47632800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:47621200-47628400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:47623400-47631600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:47624200-47630000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:47624600-47627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:47625600-47629800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:47625600-47631600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:47625800-47628200	Weak transcription	Ovary	ovary
31	chr12:47625800-47628400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr12:47625800-47628800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:47625800-47628800	Weak transcription	Fetal Intestine Small	intestine
34	chr12:47625800-47628800	Genic enhancers	A549	lung
35	chr12:47625800-47629400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:47625800-47630000	Weak transcription	HSMMtube	muscle
37	chr12:47625800-47630400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:47626000-47628800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:47626200-47628800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:47626600-47630600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:47626800-47630200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:47626800-47631000	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr12:47627000-47628400	Weak transcription	Lung	lung
44	chr12:47627000-47628600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:47627200-47630200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:47627200-47630400	Strong transcription	Primary B cells from cord blood	blood
47	chr12:47627400-47630200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:47627600-47628000	Weak transcription	Primary T cells from cord blood	blood
49	chr12:47627600-47628200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:47627600-47628600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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