Variant report

Variant	rs4902682
Chromosome Location	chr14:69433208-69433209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69328564..69331067-chr14:69432444..69435410,2	MCF-7	breast:
2	chr14:69431143..69434095-chr14:69444697..69447020,3	K562	blood:
3	chr14:69431359..69433978-chr14:69434741..69437243,2	K562	blood:
4	chr14:69412106..69413788-chr14:69432458..69434178,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259062	Chromatin interaction
ENSG00000072110	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1007407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs10083451	0.85[JPT][hapmap]
rs10137547	0.90[ASN][1000 genomes]
rs10139873	0.85[JPT][hapmap]
rs10145565	0.85[JPT][hapmap]
rs10147976	0.90[ASN][1000 genomes]
rs11158782	0.85[JPT][hapmap]
rs11158790	0.85[JPT][hapmap]
rs1147481	0.85[JPT][hapmap]
rs12432970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12434478	0.85[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12589028	0.85[JPT][hapmap]
rs1275407	0.85[JPT][hapmap]
rs17093668	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17106670	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001998	0.85[JPT][hapmap]
rs2012750	0.90[ASN][1000 genomes]
rs2012764	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2012785	0.90[ASN][1000 genomes]
rs2024892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2024893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2268968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300875	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs28561965	0.90[ASN][1000 genomes]
rs28613298	0.85[JPT][hapmap]
rs4243632	0.87[ASN][1000 genomes]
rs6573869	0.85[JPT][hapmap]
rs7140693	0.88[CHD][hapmap]
rs7146225	0.85[JPT][hapmap]
rs7149487	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7160629	0.85[JPT][hapmap]
rs72733548	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8015876	1.00[JPT][hapmap]
rs9323524	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2761842	chr14:69431091-69434387	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4902682	SMOC1	cis	cerebellum	SCAN
rs4902682	ACTN1-AS1	cis	Esophagus Muscularis	GTEx
rs4902682	PLEKHG3	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69409800-69434400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr14:69411200-69442600	Weak transcription	Fetal Brain Female	brain
3	chr14:69420200-69437200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:69420200-69441200	Genic enhancers	NHEK	skin
5	chr14:69420600-69441600	Genic enhancers	NH-A	brain
6	chr14:69421200-69442200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr14:69422400-69433600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr14:69423000-69435000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:69426000-69433600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr14:69426000-69436600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr14:69426200-69436400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr14:69426200-69436600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr14:69426200-69436800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr14:69426600-69434600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr14:69427600-69433400	Enhancers	Fetal Muscle Leg	muscle
16	chr14:69427600-69437600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr14:69427600-69437600	Enhancers	Left Ventricle	heart
18	chr14:69428400-69437200	Enhancers	Adipose Nuclei	Adipose
19	chr14:69428400-69437200	Genic enhancers	NHLF	lung
20	chr14:69428400-69442200	Genic enhancers	Fetal Stomach	stomach
21	chr14:69428600-69439800	Genic enhancers	Fetal Intestine Small	intestine
22	chr14:69428600-69443400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:69428800-69434200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr14:69429000-69433400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr14:69429000-69436200	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr14:69429200-69439600	Enhancers	Fetal Thymus	thymus
27	chr14:69429400-69443800	Weak transcription	Brain Germinal Matrix	brain
28	chr14:69429800-69434000	Enhancers	HSMMtube	muscle
29	chr14:69429800-69434800	Genic enhancers	HMEC	breast
30	chr14:69429800-69441400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr14:69429800-69442400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr14:69430000-69434800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
33	chr14:69430000-69436200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr14:69430000-69437800	Enhancers	Fetal Intestine Large	intestine
35	chr14:69430000-69438000	Enhancers	Liver	Liver
36	chr14:69430000-69440400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:69430000-69441600	Genic enhancers	HSMM	muscle
38	chr14:69430200-69435000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr14:69430200-69435400	Genic enhancers	A549	lung
40	chr14:69430200-69438800	Enhancers	Fetal Heart	heart
41	chr14:69430600-69434400	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr14:69430600-69435200	Enhancers	Stomach Mucosa	stomach
43	chr14:69430600-69437800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr14:69430800-69433800	Enhancers	Placenta	Placenta
45	chr14:69430800-69434200	Enhancers	Fetal Lung	lung
46	chr14:69430800-69434400	Strong transcription	Dnd41	blood
47	chr14:69430800-69434600	Enhancers	Small Intestine	intestine
48	chr14:69430800-69435400	Enhancers	Duodenum Mucosa	Duodenum
49	chr14:69430800-69435800	Enhancers	Gastric	stomach
50	chr14:69430800-69436200	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links