Variant report

Variant	rs2076170
Chromosome Location	chr6:35443573-35443574
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:34538773..34541747-chr6:35441442..35443633,2	K562	blood:
2	chr6:35441574..35443877-chr6:35520480..35522030,2	K562	blood:
3	chr6:35259275..35263852-chr6:35441869..35446640,5	K562	blood:
4	chr6:35429000..35431728-chr6:35441899..35443827,3	K562	blood:
5	chr6:35260730..35269335-chr6:35433870..35444063,22	MCF-7	breast:
6	chr6:35418658..35421546-chr6:35440931..35443702,2	K562	blood:
7	chr6:35412651..35414194-chr6:35442637..35444257,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000023892	Chromatin interaction
ENSG00000112039	Chromatin interaction
ENSG00000065029	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10214770	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12525930	0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs13214239	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2395626	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6907678	0.88[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7758978	0.92[CEU][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9368868	0.81[LWK][hapmap];1.00[YRI][hapmap]

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	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
2	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
3	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
4	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
5	nsv984463	chr6:35432948-35477634	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2076170	RPL10A	cis	multi-tissue	Pritchard
rs2076170	RP3-340B19.2	cis	Adipose Subcutaneous	GTEx
rs2076170	RPL10A	cis	parietal	SCAN
rs2076170	RPL10A	cis	cerebellum	SCAN
rs2076170	ZNF76	cis	cerebellum	SCAN
rs2076170	RPL10A	cis	Esophagus Muscularis	GTEx
rs2076170	TCP11	cis	thalamus	BrainEAC

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35437600-35449200	Strong transcription	Aorta	Aorta
2	chr6:35437800-35443800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:35437800-35446200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:35437800-35451000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:35438000-35455800	Weak transcription	Brain Angular Gyrus	brain
6	chr6:35438200-35444200	Strong transcription	Thymus	Thymus
7	chr6:35438200-35458000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:35438400-35443600	Strong transcription	Esophagus	oesophagus
9	chr6:35438400-35449600	Strong transcription	Gastric	stomach
10	chr6:35438800-35444200	Strong transcription	Brain Germinal Matrix	brain
11	chr6:35438800-35448200	Strong transcription	Right Ventricle	heart
12	chr6:35439200-35445000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:35439200-35447600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:35439200-35447600	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:35439200-35447800	Strong transcription	Colonic Mucosa	Colon
16	chr6:35439200-35448200	Strong transcription	Lung	lung
17	chr6:35439200-35452400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:35439200-35452600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:35439200-35453000	Weak transcription	Fetal Kidney	kidney
20	chr6:35439400-35452600	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr6:35439800-35443800	Strong transcription	NH-A	brain
22	chr6:35439800-35444200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:35439800-35444600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:35439800-35452600	Strong transcription	Fetal Intestine Small	intestine
25	chr6:35440000-35443600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr6:35440000-35444200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:35440000-35452400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:35440200-35443600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:35440200-35445000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:35440200-35447400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:35440200-35447600	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr6:35440200-35448200	Strong transcription	Ovary	ovary
33	chr6:35440200-35452200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:35440200-35452400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:35440200-35457200	Weak transcription	Psoas Muscle	Psoas
36	chr6:35440400-35443600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:35440400-35443600	Strong transcription	Adipose Nuclei	Adipose
38	chr6:35440400-35443800	Strong transcription	Fetal Brain Female	brain
39	chr6:35440400-35443800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr6:35440400-35446600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:35440400-35449400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:35440400-35452400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:35440400-35452400	Weak transcription	Hela-S3	cervix
44	chr6:35440400-35452600	Strong transcription	NHLF	lung
45	chr6:35440400-35452800	Strong transcription	Fetal Stomach	stomach
46	chr6:35440400-35453000	Strong transcription	Fetal Intestine Large	intestine
47	chr6:35440400-35455600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:35440600-35443800	Weak transcription	Stomach Mucosa	stomach
49	chr6:35440600-35445600	Weak transcription	Dnd41	blood
50	chr6:35440600-35446800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links