Variant report

Variant	rs10874744
Chromosome Location	chr1:93306317-93306318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1003116	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs10493863	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10735781	1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10747446	1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10782944	0.83[CHD][hapmap]
rs10782945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874751	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874753	0.87[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs11164791	1.00[JPT][hapmap]
rs11164796	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs11164830	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164835	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164836	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164840	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11164842	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164843	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11164844	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164845	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11577636	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11578986	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11587920	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12025792	1.00[JPT][hapmap]
rs12059883	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12060952	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12065253	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12066638	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12069727	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12074608	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12081675	0.87[CEU][hapmap]
rs12745968	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1337107	1.00[JPT][hapmap];0.90[MEX][hapmap]
rs1360366	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1535372	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs17380908	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2025100	0.83[CHD][hapmap]
rs2180976	0.86[ASN][1000 genomes]
rs2255717	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255723	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2263247	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2391177	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2481710	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2481711	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2481712	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2481713	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2481714	0.85[EUR][1000 genomes]
rs2492293	0.84[EUR][1000 genomes]
rs2492294	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2774941	0.82[CHD][hapmap]
rs2774945	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2774946	0.90[EUR][1000 genomes]
rs2774949	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2774950	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2774952	0.90[EUR][1000 genomes]
rs2774953	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2774954	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2774955	0.82[EUR][1000 genomes]
rs2774956	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2811589	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2811590	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2811591	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2811593	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2811594	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2811596	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2811597	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2811598	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811599	0.82[CHD][hapmap]
rs2811600	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2811602	0.91[CHD][hapmap]
rs2893225	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34084844	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34389767	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34398175	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35367625	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4294424	1.00[JPT][hapmap];0.90[MEX][hapmap]
rs4300228	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4308991	1.00[CHB][hapmap]
rs4351651	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4420089	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4450029	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4561051	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4592265	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847221	0.83[CHD][hapmap]
rs4847267	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs4847378	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4847384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847432	1.00[JPT][hapmap]
rs6604007	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs6604014	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs6604028	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6604029	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6604030	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6604031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6659942	0.91[CHD][hapmap]
rs6666831	0.84[CEU][hapmap]
rs6680578	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs6694051	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697543	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6698082	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698179	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6698233	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6700585	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7417198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7515257	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7517935	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7530780	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7536563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7542608	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7543964	0.82[CHD][hapmap]
rs7549341	0.86[ASN][1000 genomes]
rs7550347	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7550660	0.90[EUR][1000 genomes]
rs7551324	0.86[ASN][1000 genomes]
rs9439948	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9440127	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9440134	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs949915	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9651257	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.92[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv530047	chr1:93273425-93308213	Weak transcription Enhancers Strong transcription Active TSS 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 target site	26 gene(s)	inside rSNPs	diseases
3	nsv508393	chr1:93290513-93344924	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10874744	KIAA1107	cis	cerebellum	SCAN
rs10874744	BARHL2	cis	parietal	SCAN
rs10874744	MTF2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93299200-93310400	Strong transcription	Fetal Muscle Trunk	muscle
2	chr1:93299400-93307200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:93299400-93309200	Strong transcription	Placenta Amnion	Placenta Amnion
4	chr1:93299600-93306600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr1:93299600-93309000	Weak transcription	Esophagus	oesophagus
6	chr1:93299600-93309800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:93299600-93310000	Strong transcription	Placenta	Placenta
8	chr1:93299600-93310400	Strong transcription	Fetal Thymus	thymus
9	chr1:93299800-93310600	Strong transcription	Fetal Intestine Large	intestine
10	chr1:93299800-93311600	Strong transcription	Fetal Muscle Leg	muscle
11	chr1:93300000-93309800	Strong transcription	Thymus	Thymus
12	chr1:93300000-93310000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:93300000-93310000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:93300000-93310200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:93300200-93306600	Strong transcription	Fetal Kidney	kidney
16	chr1:93300200-93308000	Strong transcription	Colonic Mucosa	Colon
17	chr1:93300200-93309200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:93300200-93310000	Strong transcription	HSMMtube	muscle
19	chr1:93300200-93310200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr1:93300200-93310400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:93300400-93306600	Strong transcription	Lung	lung
22	chr1:93300400-93310000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:93300400-93316000	Strong transcription	Primary B cells from cord blood	blood
24	chr1:93300600-93308800	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr1:93300600-93309200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:93300600-93310000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:93300800-93309000	Weak transcription	Spleen	Spleen
28	chr1:93300800-93310000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:93300800-93310200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr1:93300800-93310200	Strong transcription	HSMM	muscle
31	chr1:93300800-93310400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:93301000-93306400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:93301000-93309600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:93301000-93309800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:93301000-93310000	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr1:93301000-93310200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:93301000-93310200	Strong transcription	Brain Germinal Matrix	brain
38	chr1:93301000-93318400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:93301400-93311600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:93301600-93310600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:93302000-93310200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:93302000-93310400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr1:93302200-93307000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:93302200-93310000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:93302400-93307000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr1:93302400-93307400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:93302400-93310200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:93302600-93310200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:93302600-93310200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:93302600-93310200	Strong transcription	Primary hematopoietic stem cells	blood

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