Variant report

Variant	rs861674
Chromosome Location	chr5:112064475-112064476
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112048029..112050157-chr5:112062177..112064729,3	K562	blood:
2	chr5:112048029..112050157-chr5:112062622..112064729,2	K562	blood:
3	chr5:112064316..112067247-chr5:112074858..112077502,2	K562	blood:
4	chr5:112063462..112066944-chr5:112067899..112070429,3	K562	blood:
5	chr5:112058449..112061248-chr5:112063741..112066202,3	K562	blood:
6	chr5:112042859..112045192-chr5:112064227..112066122,2	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10051624	0.82[EUR][1000 genomes]
rs10071425	0.81[EUR][1000 genomes]
rs10073398	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10075281	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs10075323	0.81[EUR][1000 genomes]
rs10075377	0.81[EUR][1000 genomes]
rs10076641	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10213844	0.82[EUR][1000 genomes]
rs10463643	0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1093677	0.90[CHD][hapmap]
rs11241182	0.89[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs11241183	0.82[EUR][1000 genomes]
rs11241184	0.88[EUR][1000 genomes]
rs11241185	0.81[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11749632	0.87[EUR][1000 genomes]
rs11749701	0.86[EUR][1000 genomes]
rs11954856	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12513787	0.81[EUR][1000 genomes]
rs12513804	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12518091	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12656359	0.81[EUR][1000 genomes]
rs12658609	0.83[EUR][1000 genomes]
rs12659119	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12719151	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1441375	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1465910	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs151977	0.88[CHD][hapmap]
rs1661035	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1661036	0.86[ASN][1000 genomes]
rs1816769	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1914	0.82[CEU][hapmap]
rs1974786	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2019720	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2020383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289484	0.89[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2431239	0.81[EUR][1000 genomes]
rs2431241	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs2431242	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2431512	0.85[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2439589	0.81[EUR][1000 genomes]
rs2439591	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2464803	0.84[TSI][hapmap]
rs2545162	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs2545165	0.86[CHB][hapmap]
rs2545167	0.88[CHD][hapmap]
rs2546106	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs2546108	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs2546117	0.81[EUR][1000 genomes]
rs2707763	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2707765	0.81[CEU][hapmap]
rs28578275	0.82[EUR][1000 genomes]
rs2900066	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2901844	0.81[EUR][1000 genomes]
rs2909786	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[EUR][1000 genomes]
rs2909787	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[EUR][1000 genomes]
rs2909958	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[EUR][1000 genomes]
rs2952615	0.86[CHB][hapmap]
rs35130225	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs351771	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs35414976	0.81[EUR][1000 genomes]
rs382260	0.87[CHD][hapmap]
rs3846716	0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs396321	0.92[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4099181	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41115	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs411356	0.93[CHB][hapmap];0.87[CHD][hapmap]
rs414098	0.92[CEU][hapmap]
rs42427	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs429427	0.88[CHD][hapmap]
rs430665	0.88[CHD][hapmap]
rs464002	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs464708	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs465454	0.88[CHD][hapmap]
rs465899	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs467033	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs468179	0.86[ASN][1000 genomes]
rs4705486	0.81[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4705559	0.85[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs4705573	0.81[EUR][1000 genomes]
rs4705608	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4705609	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4705610	0.85[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4705624	0.82[EUR][1000 genomes]
rs4705815	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705816	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs497844	0.88[CHD][hapmap]
rs544243	0.89[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs56335290	0.82[ASN][1000 genomes]
rs569940	0.86[EUR][1000 genomes]
rs62364017	0.89[EUR][1000 genomes]
rs6594643	0.85[CEU][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6594644	0.86[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6594646	0.85[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6862050	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs6864688	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6867243	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6879057	0.81[EUR][1000 genomes]
rs6893949	0.82[EUR][1000 genomes]
rs6894351	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]
rs6898133	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712662	0.88[CHD][hapmap]
rs712665	0.88[CHD][hapmap]
rs7704618	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs866006	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs9326862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9326863	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs953916	0.87[EUR][1000 genomes]
rs9647582	0.82[EUR][1000 genomes]
rs9647583	0.81[EUR][1000 genomes]
rs971517	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs861674	NCRNA00219	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112046000-112069200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:112047000-112066000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:112047400-112072400	Weak transcription	Thymus	Thymus
4	chr5:112052000-112072600	Weak transcription	Primary B cells from cord blood	blood
5	chr5:112052600-112072600	Weak transcription	Primary T cells from cord blood	blood
6	chr5:112054400-112073200	Weak transcription	Pancreas	Pancrea
7	chr5:112056600-112066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:112056600-112067400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr5:112057400-112064800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:112058600-112072800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:112059200-112067000	Weak transcription	Brain Anterior Caudate	brain
12	chr5:112059200-112067600	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:112059200-112073200	Weak transcription	Left Ventricle	heart
14	chr5:112060000-112072800	Weak transcription	Fetal Heart	heart
15	chr5:112060400-112064800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:112060600-112070000	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:112060800-112069200	Weak transcription	Brain Substantia Nigra	brain
18	chr5:112061000-112072800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:112061000-112072800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:112061000-112073000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:112061800-112073000	Weak transcription	Fetal Stomach	stomach
22	chr5:112062200-112067000	Weak transcription	Psoas Muscle	Psoas
23	chr5:112062200-112073000	Weak transcription	Brain Germinal Matrix	brain
24	chr5:112062400-112065000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:112062400-112072800	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:112062400-112073000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:112062400-112073000	Weak transcription	Fetal Intestine Small	intestine
28	chr5:112062800-112065000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:112063400-112066200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:112064400-112066000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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