Variant report

Variant	rs2170953
Chromosome Location	chr8:50868319-50868320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10096242	0.82[ASN][1000 genomes]
rs10112215	0.85[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10112818	0.81[ASW][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.83[AFR][1000 genomes]
rs1021202	0.85[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1023979	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs10504093	0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10957681	0.82[ASN][1000 genomes]
rs10957739	0.85[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10957741	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs1157932	0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11773979	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777957	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11781675	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11782772	0.82[ASN][1000 genomes]
rs11783503	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs11783631	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs12541061	0.85[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs12541363	0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12681482	0.83[EUR][1000 genomes]
rs13264385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13273334	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1344326	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs1352114	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs1352117	0.88[TSI][hapmap]
rs1484805	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs1484807	0.85[CEU][hapmap]
rs1484813	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1486258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1486263	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs1552378	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1552380	0.88[JPT][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs167631	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs16914039	0.82[ASN][1000 genomes]
rs170331	0.82[ASN][1000 genomes]
rs1843607	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs186455	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2015043	0.85[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2086888	0.85[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2129161	0.85[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2129169	0.85[CEU][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2200494	0.85[TSI][hapmap]
rs2220157	0.85[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2247368	0.80[ASN][1000 genomes]
rs2385554	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385696	0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2385697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385698	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2385700	0.83[EUR][1000 genomes]
rs2449960	0.80[ASN][1000 genomes]
rs2449961	0.91[ASN][1000 genomes]
rs2449963	0.85[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs2450286	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs2450287	0.83[ASN][1000 genomes]
rs2450290	0.96[CHD][hapmap];0.83[ASN][1000 genomes]
rs28869911	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs318850	0.80[ASN][1000 genomes]
rs318851	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs318853	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs318854	0.86[CHB][hapmap]
rs318858	0.82[ASN][1000 genomes]
rs318859	0.82[ASN][1000 genomes]
rs318860	0.85[TSI][hapmap]
rs318861	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs318867	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs318873	0.88[TSI][hapmap]
rs318874	0.82[ASN][1000 genomes]
rs318884	0.81[EUR][1000 genomes]
rs318885	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs318888	0.81[EUR][1000 genomes]
rs318890	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs318913	0.85[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs318915	0.85[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs318916	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs318918	0.85[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs318920	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs318923	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs365318	0.85[TSI][hapmap]
rs379601	0.87[ASN][1000 genomes]
rs3812426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs404309	0.87[ASN][1000 genomes]
rs412929	0.86[ASN][1000 genomes]
rs415276	0.87[TSI][hapmap]
rs4242456	0.87[JPT][hapmap]
rs4460388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs451034	0.87[ASN][1000 genomes]
rs453906	0.82[ASN][1000 genomes]
rs4873120	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4873123	0.87[JPT][hapmap]
rs55780592	0.99[ASN][1000 genomes]
rs6472838	0.99[ASN][1000 genomes]
rs6472839	1.00[ASN][1000 genomes]
rs6984738	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6991925	0.88[JPT][hapmap];0.83[YRI][hapmap]
rs7002291	0.82[ASN][1000 genomes]
rs7002909	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7003221	0.82[ASN][1000 genomes]
rs7004973	0.82[ASN][1000 genomes]
rs7010915	0.85[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7014520	0.85[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs73676077	0.80[ASN][1000 genomes]
rs7828900	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs7833019	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7833377	0.81[JPT][hapmap]
rs923058	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs923060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs931293	0.87[JPT][hapmap]
rs931294	0.85[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs9643685	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643689	0.81[JPT][hapmap]
rs9643692	0.85[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs967107	0.80[ASN][1000 genomes]
rs967116	0.85[TSI][hapmap]
rs971926	0.85[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs993553	0.87[JPT][hapmap]

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	esv3353749	chr8:50530807-51139242	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1022115	chr8:50864995-50981944	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv611311	chr8:50865230-50980320	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2170953	ST18	cis	parietal	SCAN
rs2170953	SNTG1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50855200-50875200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:50858400-50870200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:50858400-50871600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:50860400-50875400	Weak transcription	Fetal Intestine Small	intestine
5	chr8:50865800-50869200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr8:50866000-50868600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr8:50866200-50868400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr8:50866200-50868600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr8:50866200-50868600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr8:50866600-50868400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr8:50867800-50868400	Enhancers	H9 Cell Line	embryonic stem cell
12	chr8:50867800-50868400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr8:50867800-50868400	Enhancers	Brain Anterior Caudate	brain
14	chr8:50867800-50868400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr8:50867800-50868400	Enhancers	HMEC	breast
16	chr8:50867800-50868600	Enhancers	Brain Germinal Matrix	brain
17	chr8:50867800-50869200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr8:50868000-50868400	Enhancers	Brain Hippocampus Middle	brain
19	chr8:50868000-50868600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr8:50868200-50869400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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