Variant report

Variant	rs6704188
Chromosome Location	chr1:114108711-114108712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10745339	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.96[ASN][1000 genomes]
rs10858000	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.96[ASN][1000 genomes]
rs10858001	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10858002	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10858005	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10858007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs10858008	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs10858011	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs10858017	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs11102648	0.96[ASN][1000 genomes]
rs11102649	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11102651	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102652	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.99[ASN][1000 genomes]
rs11102653	0.98[ASN][1000 genomes]
rs11102654	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11102657	0.90[ASN][1000 genomes]
rs11102658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102661	0.93[ASN][1000 genomes]
rs11102669	0.92[ASN][1000 genomes]
rs1113523	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.96[ASN][1000 genomes]
rs1146180	0.80[ASN][1000 genomes]
rs1146182	0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap];0.93[ASN][1000 genomes]
rs1146187	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs12021513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12035317	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.99[ASN][1000 genomes]
rs12037873	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12039224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12043639	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12061482	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs12074958	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.99[ASN][1000 genomes]
rs12077419	1.00[ASN][1000 genomes]
rs1217192	0.90[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs1217193	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1217199	0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1217200	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs1217201	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs1217203	0.95[ASN][1000 genomes]
rs1217204	0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs1217208	0.95[ASN][1000 genomes]
rs1217210	0.93[ASN][1000 genomes]
rs1217211	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1217214	0.93[ASN][1000 genomes]
rs1217215	0.95[ASN][1000 genomes]
rs1217221	0.87[ASN][1000 genomes]
rs1217223	0.95[ASN][1000 genomes]
rs1217226	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs1217227	0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs1217228	0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs1217230	0.95[ASN][1000 genomes]
rs1217232	0.95[ASN][1000 genomes]
rs1217233	0.95[ASN][1000 genomes]
rs1217234	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs1217235	0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1217236	0.90[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs1217237	0.95[ASN][1000 genomes]
rs1228280	0.92[ASN][1000 genomes]
rs1230640	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs1230645	0.81[CHB][hapmap]
rs1230647	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs1230649	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs1230655	0.92[ASN][1000 genomes]
rs1230656	0.86[ASN][1000 genomes]
rs1230658	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs1230659	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs1230661	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1230663	0.86[ASN][1000 genomes]
rs1230671	0.93[ASN][1000 genomes]
rs1230685	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs1235687	0.96[ASN][1000 genomes]
rs1235688	0.95[ASN][1000 genomes]
rs1237289	0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12565589	0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs1343125	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs1343128	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs1343629	0.85[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1418957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1418958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013326	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.96[ASN][1000 genomes]
rs17031716	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1743605	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs1777234	0.93[ASN][1000 genomes]
rs1777237	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs1777238	0.92[ASN][1000 genomes]
rs1777241	0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.91[ASN][1000 genomes]
rs1936398	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs1981319	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs2093436	0.81[CHB][hapmap]
rs2153977	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2295853	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs2359167	0.81[CHB][hapmap]
rs2636002	0.88[ASN][1000 genomes]
rs2636013	0.81[CHB][hapmap]
rs2797412	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs2798135	0.93[ASN][1000 genomes]
rs2798138	0.93[ASN][1000 genomes]
rs2884703	0.99[ASN][1000 genomes]
rs2884704	0.93[ASN][1000 genomes]
rs4259646	0.81[YRI][hapmap]
rs4274063	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4456089	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.95[ASN][1000 genomes]
rs4600045	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs4838997	0.92[ASN][1000 genomes]
rs4839335	0.87[ASN][1000 genomes]
rs6537790	0.81[YRI][hapmap]
rs6537792	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6689879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6698586	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs72687973	0.89[ASN][1000 genomes]
rs72687980	1.00[ASN][1000 genomes]
rs7536360	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7554019	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv437013	chr1:114065955-114129092	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv947128	chr1:114088844-114122533	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6704188	BCL2L15	cis	cerebellum	SCAN
rs6704188	DENND2C	cis	parietal	SCAN
rs6704188	MAGI3	cis	cerebellum	SCAN
rs6704188	PHTF1	cis	cerebellum	SCAN
rs6704188	MAGI3	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114083400-114110000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:114088600-114109800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:114094800-114138400	Weak transcription	NHDF-Ad	bronchial
4	chr1:114096400-114108800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:114100200-114127600	Weak transcription	Ovary	ovary
6	chr1:114100600-114108800	Weak transcription	Fetal Lung	lung
7	chr1:114100600-114112600	Weak transcription	Esophagus	oesophagus
8	chr1:114100600-114118200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:114100600-114118600	Weak transcription	Lung	lung
10	chr1:114100600-114118800	Weak transcription	Pancreas	Pancrea
11	chr1:114100600-114140200	Weak transcription	Left Ventricle	heart
12	chr1:114100600-114173400	Weak transcription	Gastric	stomach
13	chr1:114100800-114109600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:114101000-114112600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:114105600-114109600	Weak transcription	Right Ventricle	heart
16	chr1:114107600-114109000	Enhancers	Dnd41	blood
17	chr1:114107800-114110400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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