Variant report

Variant	rs9395878
Chromosome Location	chr6:53668237-53668238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53658074..53661500-chr6:53665501..53670163,6	MCF-7	breast:
2	chr6:53668227..53671026-chr6:53671811..53674151,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10456672	0.84[AMR][1000 genomes]
rs10755766	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1076701	0.94[CEU][hapmap];0.81[MEX][hapmap]
rs1076702	0.94[CEU][hapmap]
rs10948775	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11751003	0.83[AMR][1000 genomes]
rs11758147	0.84[AMR][1000 genomes]
rs13216331	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes]
rs2073020	0.83[AMR][1000 genomes]
rs2294790	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2294791	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3777661	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4314499	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4345397	0.85[AMR][1000 genomes]
rs4373352	0.85[AMR][1000 genomes]
rs4400206	0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs4404762	0.85[AMR][1000 genomes]
rs4441952	0.84[AMR][1000 genomes]
rs4457161	0.83[AMR][1000 genomes]
rs4516937	0.87[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes]
rs4563705	0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes]
rs4610551	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4712043	0.83[AMR][1000 genomes]
rs4712044	0.82[AMR][1000 genomes]
rs4715418	0.83[AMR][1000 genomes]
rs6903399	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6908232	0.85[AMR][1000 genomes]
rs6921605	0.83[TSI][hapmap]
rs6925356	0.83[AMR][1000 genomes]
rs6934324	0.84[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs7749273	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs7763482	0.87[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs7776124	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs9349685	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9357776	0.94[CEU][hapmap]
rs9370233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370241	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9370244	0.83[AMR][1000 genomes]
rs9382231	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9382232	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9382233	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9382235	0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9382238	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382241	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382243	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382244	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382246	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382248	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9382252	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382253	0.85[EUR][1000 genomes]
rs9382254	1.00[CEU][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs9382256	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9395876	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9395881	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9474641	0.83[AMR][1000 genomes]
rs9474646	0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9395878	HMGCLL1	cis	parietal	SCAN
rs9395878	ZNF451	cis	parietal	SCAN
rs9395878	LRRC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53669800	Weak transcription	Gastric	stomach
2	chr6:53661400-53670400	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
5	chr6:53662000-53670200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:53662600-53669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:53662600-53670000	Weak transcription	Esophagus	oesophagus
8	chr6:53662600-53670400	Weak transcription	Thymus	Thymus
9	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
10	chr6:53662800-53669800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:53662800-53669800	Weak transcription	HMEC	breast
12	chr6:53662800-53670200	Weak transcription	Fetal Intestine Large	intestine
13	chr6:53662800-53670200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:53662800-53675400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:53663000-53669800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:53663200-53670600	Weak transcription	Fetal Intestine Small	intestine
17	chr6:53664000-53669000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:53664800-53668400	Weak transcription	HepG2	liver
19	chr6:53664800-53669800	Weak transcription	Fetal Thymus	thymus
20	chr6:53664800-53673400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:53665000-53669800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:53665000-53674800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:53665000-53675600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:53665800-53668800	Enhancers	Dnd41	blood
25	chr6:53666000-53670000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:53666200-53669800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:53666800-53669000	Enhancers	NHLF	lung
28	chr6:53667000-53669800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:53667000-53670000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:53667000-53670200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:53667200-53669000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:53667400-53668800	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr6:53667400-53669600	Weak transcription	Aorta	Aorta
34	chr6:53667600-53668600	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:53667600-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:53667800-53668400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:53667800-53668600	Weak transcription	Brain Germinal Matrix	brain
38	chr6:53667800-53668800	Enhancers	Lung	lung
39	chr6:53667800-53668800	Enhancers	Rectal Smooth Muscle	rectum
40	chr6:53667800-53669000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr6:53667800-53670000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:53667800-53673600	Enhancers	Brain Substantia Nigra	brain
43	chr6:53668000-53668800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:53668000-53668800	Enhancers	Pancreas	Pancrea
45	chr6:53668000-53668800	Enhancers	HUVEC	blood vessel
46	chr6:53668000-53669000	Enhancers	NH-A	brain
47	chr6:53668000-53670200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:53668000-53670800	Enhancers	NHEK	skin
49	chr6:53668000-53671400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr6:53668200-53668600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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