Variant report

Variant	rs4713854
Chromosome Location	chr6:35381099-35381100
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35380537..35383478-chr6:35394277..35398227,3	K562	blood:
2	chr6:35379744..35382549-chr6:35384456..35386159,2	K562	blood:
3	chr6:35311343..35313343-chr6:35379052..35381672,2	MCF-7	breast:
4	chr6:35369022..35371530-chr6:35380488..35382015,2	MCF-7	breast:
5	chr6:35374379..35377300-chr6:35379343..35382186,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4713842	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs4713843	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs4713846	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs707969	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs72909084	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv470812	chr6:35374461-35418118	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
7	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
8	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
9	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
10	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4713854	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35360000-35382600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:35361800-35385800	Weak transcription	Small Intestine	intestine
3	chr6:35366200-35386800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:35366400-35382800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:35369200-35382600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:35369400-35382600	Weak transcription	NH-A	brain
7	chr6:35370600-35393200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:35371000-35382400	Weak transcription	Right Atrium	heart
9	chr6:35371200-35382400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:35371200-35382400	Weak transcription	Stomach Mucosa	stomach
11	chr6:35371200-35383200	Weak transcription	Fetal Kidney	kidney
12	chr6:35372000-35382400	Weak transcription	Fetal Heart	heart
13	chr6:35373200-35381400	Weak transcription	Fetal Brain Male	brain
14	chr6:35373400-35382400	Weak transcription	Brain Germinal Matrix	brain
15	chr6:35375200-35382600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:35375600-35387000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:35377600-35381200	Strong transcription	Liver	Liver
18	chr6:35377600-35382400	Strong transcription	Fetal Muscle Leg	muscle
19	chr6:35377600-35382400	Strong transcription	Osteobl	bone
20	chr6:35377600-35386000	Weak transcription	HUVEC	blood vessel
21	chr6:35377800-35385600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:35377800-35395000	Weak transcription	K562	blood
23	chr6:35378000-35381200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr6:35378000-35381200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:35378000-35381400	Strong transcription	Gastric	stomach
26	chr6:35378000-35381400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr6:35378000-35381800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr6:35378000-35382400	Strong transcription	Fetal Stomach	stomach
29	chr6:35378000-35382600	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:35378000-35386400	Strong transcription	Spleen	Spleen
31	chr6:35378200-35381200	Strong transcription	Brain Cingulate Gyrus	brain
32	chr6:35378200-35381800	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:35378200-35382400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:35378200-35382400	Strong transcription	Esophagus	oesophagus
35	chr6:35378200-35382800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:35378400-35381400	Strong transcription	HSMMtube	muscle
37	chr6:35378400-35381800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:35378400-35381800	Strong transcription	Brain Anterior Caudate	brain
39	chr6:35378400-35381800	Strong transcription	Brain Hippocampus Middle	brain
40	chr6:35378400-35382000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:35378400-35382200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:35378400-35385600	Strong transcription	Fetal Intestine Small	intestine
43	chr6:35378400-35386800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr6:35378600-35381200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:35378600-35381200	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:35378600-35381200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr6:35378600-35381200	Strong transcription	Colonic Mucosa	Colon
48	chr6:35378600-35381200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:35378600-35381400	Strong transcription	Ovary	ovary
50	chr6:35378600-35381800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links