Variant report

Variant	rs17831310
Chromosome Location	chr6:56726642-56726643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56726286..56729119-chr6:56729880..56733046,4	MCF-7	breast:
2	chr6:56725702..56727982-chr6:56732126..56734324,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BEND6-1	chr6:56726626-56726713	ENSG00000231441.1
2	lnc-BEND6-1	chr6:56726626-56726713	NONHSAT113249
3	lnc-BEND6-1	chr6:56726642-56726713	NONHSAT113250

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16888081	1.00[EUR][1000 genomes]
rs16888189	0.91[CHB][hapmap]
rs16888192	0.91[CHB][hapmap]
rs4074103	0.89[JPT][hapmap]
rs4568454	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4587171	0.83[CHB][hapmap];0.81[JPT][hapmap];0.84[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17831310	RPA1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56716800-56727200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:56717000-56727200	Weak transcription	Psoas Muscle	Psoas
3	chr6:56717400-56730200	Weak transcription	Ovary	ovary
4	chr6:56717800-56727000	Weak transcription	GM12878-XiMat	blood
5	chr6:56717800-56727400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:56717800-56730400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:56718200-56731000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:56721200-56727400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr6:56721200-56727800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:56721800-56731200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:56723000-56732600	Weak transcription	Small Intestine	intestine
12	chr6:56724200-56733800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:56724600-56728000	Enhancers	HSMMtube	muscle
14	chr6:56724600-56728600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr6:56724600-56730400	Enhancers	Fetal Intestine Small	intestine
16	chr6:56724800-56727200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr6:56724800-56727200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:56725000-56730400	Enhancers	HUVEC	blood vessel
19	chr6:56725200-56728600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:56725400-56727000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:56725400-56727600	Weak transcription	NHEK	skin
22	chr6:56725600-56727000	Weak transcription	Osteobl	bone
23	chr6:56725600-56727200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:56725600-56727200	Enhancers	A549	lung
25	chr6:56725600-56727600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:56725600-56727600	Weak transcription	HMEC	breast
27	chr6:56725600-56730000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:56725600-56730200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:56725600-56731000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:56725600-56731200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:56725600-56734800	Enhancers	Hela-S3	cervix
32	chr6:56725800-56726800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:56725800-56726800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:56725800-56727200	Weak transcription	Left Ventricle	heart
35	chr6:56725800-56727200	Weak transcription	NH-A	brain
36	chr6:56725800-56727400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:56725800-56727400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:56725800-56730400	Enhancers	Fetal Intestine Large	intestine
39	chr6:56726000-56727200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:56726000-56727200	Genic enhancers	NHLF	lung
41	chr6:56726200-56727400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:56726200-56727400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:56726200-56728000	Genic enhancers	HSMM	muscle
44	chr6:56726400-56727400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:56726600-56727200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:56726600-56727200	Genic enhancers	NHDF-Ad	bronchial
47	chr6:56726600-56730000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links