Variant report

Variant	rs6846936
Chromosome Location	chr4:120137964-120137965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119603174..119605394-chr4:120137644..120139212,2	K562	blood:
2	chr4:120136077..120139007-chr4:120191556..120193518,2	K562	blood:
3	chr4:120135683..120139128-chr4:120180501..120183210,3	K562	blood:
4	chr4:120135683..120138360-chr4:120179744..120182686,3	K562	blood:
5	chr4:120132080..120136189-chr4:120136407..120141066,11	MCF-7	breast:
6	chr4:120136237..120140737-chr4:120147652..120152174,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11725433	0.90[ASN][1000 genomes]
rs11729857	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11733606	0.90[ASN][1000 genomes]
rs11737560	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13104050	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13106878	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113462	0.90[ASN][1000 genomes]
rs13113662	0.90[ASN][1000 genomes]
rs13127517	0.81[ASN][1000 genomes]
rs13140255	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13144426	0.90[ASN][1000 genomes]
rs1511021	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511022	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334151	0.90[ASN][1000 genomes]
rs17517075	0.85[ASN][1000 genomes]
rs34156358	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34478210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34624042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34951506	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35137697	0.90[ASN][1000 genomes]
rs35612705	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35646004	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35830965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62328380	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62328402	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62328403	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62328404	0.90[ASN][1000 genomes]
rs71610255	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655064	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7678138	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6846936	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs6846936	USP53	cis	Whole Blood	GTEx
rs6846936	RP11-33B1.1	cis	Thyroid	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120132600-120138200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:120134600-120144600	Weak transcription	Spleen	Spleen
3	chr4:120134800-120138800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:120134800-120142000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:120134800-120143400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:120134800-120147000	Weak transcription	Fetal Brain Male	brain
7	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:120135000-120138400	Weak transcription	Gastric	stomach
9	chr4:120135000-120142600	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:120135000-120142800	Weak transcription	Lung	lung
11	chr4:120135000-120154800	Weak transcription	Primary B cells from cord blood	blood
12	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:120135200-120138400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:120135200-120138400	Weak transcription	Fetal Thymus	thymus
16	chr4:120135200-120138600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr4:120135200-120139000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:120135200-120139000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:120135200-120139000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:120135200-120140400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:120135200-120140400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:120135200-120142000	Weak transcription	Esophagus	oesophagus
23	chr4:120135200-120142000	Weak transcription	Ovary	ovary
24	chr4:120135200-120143200	Weak transcription	Brain Substantia Nigra	brain
25	chr4:120135200-120143600	Weak transcription	Thymus	Thymus
26	chr4:120135200-120155000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:120135200-120155000	Weak transcription	Small Intestine	intestine
28	chr4:120135200-120163600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:120135400-120138400	Weak transcription	Psoas Muscle	Psoas
32	chr4:120135400-120138800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr4:120135400-120138800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:120135400-120138800	Weak transcription	Placenta	Placenta
35	chr4:120135400-120142400	Weak transcription	Fetal Intestine Small	intestine
36	chr4:120135400-120159000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:120135600-120138800	Weak transcription	Fetal Intestine Large	intestine
39	chr4:120135600-120141800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr4:120135600-120142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:120135600-120142800	Weak transcription	Fetal Stomach	stomach
42	chr4:120135600-120155000	Weak transcription	K562	blood
43	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
44	chr4:120135800-120139000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:120135800-120140000	Weak transcription	Fetal Lung	lung
46	chr4:120136000-120138200	Weak transcription	Fetal Heart	heart
47	chr4:120136000-120138800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:120136000-120145600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:120136200-120138400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:120136200-120138400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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