Variant report

Variant	rs6871895
Chromosome Location	chr5:16784785-16784786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16756542..16758777-chr5:16782954..16785752,2	K562	blood:
2	chr5:16782557..16785455-chr5:16934978..16937136,2	MCF-7	breast:
3	chr5:16784701..16787932-chr5:16789785..16793090,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13178744	1.00[CHD][hapmap]
rs16869172	1.00[AMR][1000 genomes]
rs17614462	1.00[CHD][hapmap]
rs60507141	1.00[AMR][1000 genomes]
rs60716563	1.00[AMR][1000 genomes]
rs6865207	0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6870170	1.00[AMR][1000 genomes]
rs747058	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880373	chr5:16710572-16785604	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3529928	chr5:16748426-16856563	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv3529929	chr5:16748426-16856563	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv964758	chr5:16783252-16787402	Weak transcription Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6871895	NRIP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16755200-16795400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:16757600-16796800	Weak transcription	Right Ventricle	heart
3	chr5:16760000-16791400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:16761000-16796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:16763800-16794600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:16764600-16792800	Weak transcription	Stomach Mucosa	stomach
7	chr5:16764600-16807400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:16766800-16785200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:16770200-16791400	Weak transcription	Fetal Kidney	kidney
10	chr5:16770800-16792400	Weak transcription	Placenta	Placenta
11	chr5:16770800-16793800	Weak transcription	Hela-S3	cervix
12	chr5:16775200-16796800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:16776200-16785400	Strong transcription	HUVEC	blood vessel
14	chr5:16776800-16784800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr5:16777200-16785600	Strong transcription	Fetal Intestine Small	intestine
16	chr5:16777800-16785200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:16777800-16786200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:16778800-16800000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:16779200-16785000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:16779400-16785200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:16779400-16785400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:16779400-16791400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:16779800-16796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:16779800-16797200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:16780200-16791000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:16780800-16791400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:16781800-16785200	Strong transcription	Fetal Lung	lung
28	chr5:16781800-16785200	Strong transcription	NHEK	skin
29	chr5:16781800-16786400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:16782000-16785400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr5:16782400-16786600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:16783000-16788200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:16783000-16797000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:16783000-16797400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:16783200-16784800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:16783200-16791400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:16783400-16784800	Weak transcription	Fetal Brain Male	brain
38	chr5:16783400-16792600	Weak transcription	Lung	lung
39	chr5:16783400-16796800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:16783400-16810000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:16783600-16785400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:16783600-16785800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr5:16783600-16785800	Enhancers	NHDF-Ad	bronchial
44	chr5:16783800-16784800	Genic enhancers	Gastric	stomach
45	chr5:16783800-16784800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr5:16783800-16785000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr5:16783800-16785200	Enhancers	Adipose Nuclei	Adipose
48	chr5:16783800-16785400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:16783800-16785400	Enhancers	Spleen	Spleen
50	chr5:16783800-16785400	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links