Variant report

Variant	rs2523882
Chromosome Location	chr6:31042217-31042218
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	chr6:31027525..31029714-chr6:31040492..31042279,2	K562	blood:

Extended variants
information (count: 118 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs2106067	0.86[ASN][1000 genomes]
rs2246330	0.87[ASN][1000 genomes]
rs2249231	0.87[ASN][1000 genomes]
rs2249485	0.86[ASN][1000 genomes]
rs2249486	0.86[ASN][1000 genomes]
rs2249876	0.86[ASN][1000 genomes]
rs2394420	0.86[ASN][1000 genomes]
rs2428520	0.87[ASN][1000 genomes]
rs2429721	0.80[ASN][1000 genomes]
rs2517414	0.81[ASN][1000 genomes]
rs2517423	0.81[ASN][1000 genomes]
rs2517427	0.81[ASN][1000 genomes]
rs2517440	0.81[ASN][1000 genomes]
rs2517450	0.82[ASN][1000 genomes]
rs2517452	0.82[ASN][1000 genomes]
rs2517453	0.82[ASN][1000 genomes]
rs2517455	0.82[ASN][1000 genomes]
rs2517458	0.82[ASN][1000 genomes]
rs2517460	0.82[ASN][1000 genomes]
rs2517464	0.80[ASN][1000 genomes]
rs2517465	0.82[ASN][1000 genomes]
rs2517470	0.82[ASN][1000 genomes]
rs2517471	0.86[ASN][1000 genomes]
rs2517472	0.86[ASN][1000 genomes]
rs2517475	0.84[ASN][1000 genomes]
rs2517476	0.85[ASN][1000 genomes]
rs2517477	0.86[ASN][1000 genomes]
rs2517478	0.86[ASN][1000 genomes]
rs2517480	0.85[ASN][1000 genomes]
rs2517483	0.87[ASN][1000 genomes]
rs2517488	0.87[ASN][1000 genomes]
rs2517489	0.87[ASN][1000 genomes]
rs2517492	0.87[ASN][1000 genomes]
rs2517493	0.87[ASN][1000 genomes]
rs2517497	0.87[ASN][1000 genomes]
rs2517541	0.81[ASN][1000 genomes]
rs2523836	0.86[ASN][1000 genomes]
rs2523843	0.84[ASN][1000 genomes]
rs2523860	0.86[ASN][1000 genomes]
rs2523878	0.85[ASN][1000 genomes]
rs2523880	0.87[ASN][1000 genomes]
rs2523881	0.87[ASN][1000 genomes]
rs2523883	0.88[ASN][1000 genomes]
rs2523884	0.87[ASN][1000 genomes]
rs2523885	0.87[ASN][1000 genomes]
rs2523886	0.87[ASN][1000 genomes]
rs2523888	0.87[ASN][1000 genomes]
rs2523889	0.87[ASN][1000 genomes]
rs2523890	0.86[ASN][1000 genomes]
rs2523891	0.87[ASN][1000 genomes]
rs2523893	0.87[ASN][1000 genomes]
rs2523894	0.87[ASN][1000 genomes]
rs2523895	0.86[ASN][1000 genomes]
rs2523896	0.87[ASN][1000 genomes]
rs2535282	0.81[ASN][1000 genomes]
rs2535283	0.81[ASN][1000 genomes]
rs2535287	0.81[ASN][1000 genomes]
rs2535288	0.80[ASN][1000 genomes]
rs2535289	0.81[ASN][1000 genomes]
rs2535290	0.81[ASN][1000 genomes]
rs2535291	0.81[ASN][1000 genomes]
rs2535292	0.82[ASN][1000 genomes]
rs2535293	0.82[ASN][1000 genomes]
rs2535297	0.82[ASN][1000 genomes]
rs2535299	0.82[ASN][1000 genomes]
rs2535301	0.82[ASN][1000 genomes]
rs2535302	0.82[ASN][1000 genomes]
rs2535303	0.85[ASN][1000 genomes]
rs2535304	0.86[ASN][1000 genomes]
rs2535305	0.86[ASN][1000 genomes]
rs2535306	0.86[ASN][1000 genomes]
rs2535307	0.86[ASN][1000 genomes]
rs2535308	0.86[ASN][1000 genomes]
rs2535309	0.86[ASN][1000 genomes]
rs2535310	0.86[ASN][1000 genomes]
rs2535311	0.86[ASN][1000 genomes]
rs2535312	0.86[ASN][1000 genomes]
rs2535313	0.86[ASN][1000 genomes]
rs2535314	0.86[ASN][1000 genomes]
rs2535315	0.86[ASN][1000 genomes]
rs2844641	0.87[ASN][1000 genomes]
rs2905759	0.85[ASN][1000 genomes]
rs3095305	0.81[ASN][1000 genomes]
rs3130546	0.81[ASN][1000 genomes]
rs3130957	0.83[ASN][1000 genomes]
rs3130959	0.83[ASN][1000 genomes]
rs3130960	0.82[ASN][1000 genomes]
rs3130961	0.82[ASN][1000 genomes]
rs3130963	0.82[ASN][1000 genomes]
rs3130964	0.81[ASN][1000 genomes]
rs3130970	0.81[ASN][1000 genomes]
rs6921557	0.82[ASN][1000 genomes]
rs6940894	0.83[ASN][1000 genomes]
rs6941772	0.86[ASN][1000 genomes]
rs9263456	0.86[ASN][1000 genomes]
rs9263465	0.85[ASN][1000 genomes]
rs9263466	0.85[ASN][1000 genomes]
rs9263473	0.86[ASN][1000 genomes]
rs9263474	0.86[ASN][1000 genomes]
rs9263475	0.89[AFR][1000 genomes]
rs9263493	0.82[ASN][1000 genomes]
rs9263494	0.82[ASN][1000 genomes]
rs9263593	0.80[ASN][1000 genomes]
rs9263597	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv884132	chr6:31014305-31057183	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
10	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
11	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
12	nsv884134	chr6:31028345-31048263	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
13	nsv884135	chr6:31034264-31044522	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv884136	chr6:31036783-31044522	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2523882	HCG22	cis	Lymphoblastoid	GTEx
rs2523882	hmm31752	cis	multi-tissue	Pritchard
rs2523882	ZNF204P	cis	cerebellum	SCAN
rs2523882	HCG22	cis	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31022200-31050800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:31037000-31047400	Weak transcription	Right Atrium	heart
3	chr6:31038600-31047400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:31039000-31044600	Weak transcription	Fetal Kidney	kidney
5	chr6:31039000-31047400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:31039000-31047400	Weak transcription	Fetal Brain Male	brain
7	chr6:31039000-31047400	Weak transcription	HMEC	breast
8	chr6:31039000-31048200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:31039200-31047400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:31039200-31047400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:31040000-31042400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:31040200-31047400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:31040400-31047200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:31040400-31047400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:31040600-31042600	Weak transcription	HSMMtube	muscle
16	chr6:31040600-31042800	Weak transcription	Stomach Mucosa	stomach
17	chr6:31040600-31043200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:31040600-31043200	Weak transcription	HSMM	muscle
19	chr6:31040600-31047200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:31040600-31047400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:31040600-31047400	Weak transcription	Esophagus	oesophagus
22	chr6:31040600-31047400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr6:31040600-31047400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr6:31040600-31047400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:31040600-31055000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:31040600-31062400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:31040800-31047400	Weak transcription	Brain Anterior Caudate	brain
28	chr6:31040800-31047400	Weak transcription	HUVEC	blood vessel
29	chr6:31041000-31043400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:31041000-31047200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:31041000-31047400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:31041400-31042400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr6:31041600-31042400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:31041600-31043000	Weak transcription	NHDF-Ad	bronchial
35	chr6:31041600-31043200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:31041600-31043200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:31041600-31043200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:31041600-31043200	Weak transcription	Osteobl	bone
39	chr6:31041600-31043400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:31041600-31047400	Weak transcription	Brain Germinal Matrix	brain
41	chr6:31041600-31047400	Weak transcription	Fetal Lung	lung
42	chr6:31041600-31047400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:31041600-31047400	Weak transcription	GM12878-XiMat	blood
44	chr6:31041600-31047400	Weak transcription	Hela-S3	cervix
45	chr6:31041600-31053200	Weak transcription	NH-A	brain
46	chr6:31041800-31042600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr6:31041800-31043200	Weak transcription	NHLF	lung
48	chr6:31041800-31047400	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:31042200-31042400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:31042200-31042600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links