Variant report

Variant	rs6894351
Chromosome Location	chr5:112045132-112045133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112044064..112046268-chr5:112246769..112248546,2	K562	blood:
2	chr5:112041577..112049243-chr5:112069735..112074802,8	K562	blood:
3	chr5:111887498..111890102-chr5:112044744..112046649,2	MCF-7	breast:
4	chr5:112041486..112046402-chr5:112068342..112076365,12	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10051624	0.81[EUR][1000 genomes]
rs10073398	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10075281	0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs10075323	0.80[EUR][1000 genomes]
rs10075377	0.80[EUR][1000 genomes]
rs10076641	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213844	0.81[EUR][1000 genomes]
rs10463643	0.85[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1093677	0.80[CHD][hapmap]
rs11241182	0.89[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs11241183	0.81[EUR][1000 genomes]
rs11241184	0.87[EUR][1000 genomes]
rs11241185	0.81[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs11749632	0.86[EUR][1000 genomes]
rs11749701	0.85[EUR][1000 genomes]
rs11954856	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12513787	0.80[EUR][1000 genomes]
rs12513804	0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12518091	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs12656359	0.81[EUR][1000 genomes]
rs12658609	0.82[EUR][1000 genomes]
rs12659119	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12719151	0.85[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1441375	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1465910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1661035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1661036	1.00[ASN][1000 genomes]
rs1816769	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1914	0.82[CEU][hapmap]
rs1974786	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2019720	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2020383	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2289484	0.89[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2431239	0.80[EUR][1000 genomes]
rs2431241	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs2431242	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2431512	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs2439589	0.80[EUR][1000 genomes]
rs2439591	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap]
rs2464803	0.85[TSI][hapmap]
rs2545162	0.81[CHD][hapmap]
rs2546106	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs2546108	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs2546117	0.80[EUR][1000 genomes]
rs2707763	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2707765	0.81[CEU][hapmap]
rs28578275	0.81[EUR][1000 genomes]
rs2900066	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2901844	0.80[EUR][1000 genomes]
rs2909786	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs2909787	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs2909958	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs35130225	0.91[EUR][1000 genomes]
rs351771	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs35414976	0.80[EUR][1000 genomes]
rs3846716	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396321	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4099181	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41115	0.85[CHB][hapmap]
rs411356	0.85[CHB][hapmap]
rs414098	0.92[CEU][hapmap]
rs42427	0.85[CHB][hapmap]
rs464002	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs464708	0.81[CHD][hapmap]
rs465899	0.85[CHB][hapmap]
rs467033	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs468179	1.00[ASN][1000 genomes]
rs4705486	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4705559	0.85[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4705573	0.80[EUR][1000 genomes]
rs4705608	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4705609	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705610	0.85[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4705624	0.81[EUR][1000 genomes]
rs4705815	0.85[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4705816	0.85[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs544243	0.89[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs56335290	0.89[ASN][1000 genomes]
rs569940	0.86[EUR][1000 genomes]
rs62364017	0.88[EUR][1000 genomes]
rs6594643	0.85[CEU][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6594644	0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6594646	0.85[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs6862050	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs6864688	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6867243	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6879057	0.81[EUR][1000 genomes]
rs6893949	0.81[EUR][1000 genomes]
rs6898133	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704618	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs861674	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9326862	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9326863	0.96[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs953916	0.86[EUR][1000 genomes]
rs9647582	0.81[EUR][1000 genomes]
rs9647583	0.81[EUR][1000 genomes]
rs971517	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6894351	NCRNA00219	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112042600-112045200	Active TSS	Ovary	ovary
2	chr5:112042600-112046200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr5:112042800-112045200	Active TSS	Aorta	Aorta
4	chr5:112042800-112045200	Active TSS	Colonic Mucosa	Colon
5	chr5:112042800-112045400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:112042800-112045800	Active TSS	Brain Cingulate Gyrus	brain
7	chr5:112043000-112045200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:112043000-112045400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr5:112043000-112045600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:112043000-112045600	Active TSS	HSMM	muscle
11	chr5:112043000-112045800	Active TSS	HSMMtube	muscle
12	chr5:112043000-112046000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:112043000-112048200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:112043200-112045200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr5:112043200-112045200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:112043800-112045200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr5:112043800-112045200	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr5:112043800-112045200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:112043800-112045200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr5:112043800-112045200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr5:112044000-112045200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:112044000-112045200	Flanking Active TSS	Dnd41	blood
23	chr5:112044200-112045200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:112044200-112045200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:112044200-112045200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:112044200-112045200	Weak transcription	Lung	lung
27	chr5:112044200-112045200	Weak transcription	Pancreas	Pancrea
28	chr5:112044200-112045200	Weak transcription	Small Intestine	intestine
29	chr5:112044200-112045400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:112044200-112045600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:112044200-112046600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:112044200-112046600	Weak transcription	Gastric	stomach
33	chr5:112044200-112047000	Enhancers	Primary B cells from peripheral blood	blood
34	chr5:112044200-112049400	Weak transcription	Esophagus	oesophagus
35	chr5:112044400-112045200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr5:112044400-112045400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr5:112044400-112045400	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr5:112044400-112045400	Enhancers	Placenta Amnion	Placenta Amnion
39	chr5:112044400-112045400	Flanking Active TSS	Hela-S3	cervix
40	chr5:112044400-112045600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:112044400-112045800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr5:112044400-112046000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:112044400-112046200	Enhancers	Stomach Mucosa	stomach
44	chr5:112044400-112046800	Enhancers	Spleen	Spleen
45	chr5:112044400-112047000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:112044400-112049200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr5:112044400-112049800	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr5:112044600-112045400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:112044600-112045400	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr5:112044600-112045600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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