Variant report

Variant	rs10912773
Chromosome Location	chr1:174343705-174343706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10218528	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10912797	0.85[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs10912807	0.85[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs12074753	0.85[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs12077622	0.85[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs12079820	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12084119	0.85[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs12088073	0.85[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs12568655	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12691474	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17301013	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs2006197	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2038025	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2049991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2049992	0.88[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs2064149	0.88[CEU][hapmap]
rs2143114	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs3737651	0.85[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs4442420	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4447042	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4650989	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs4650990	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs4652234	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs4652274	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56188862	0.86[EUR][1000 genomes]
rs60363188	0.83[AMR][1000 genomes]
rs6425279	0.88[CEU][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap]
rs6425280	0.85[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs6425281	0.85[CEU][hapmap]
rs6425282	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs6425283	0.84[CEU][hapmap]
rs6425284	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs6656188	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs6663591	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6666767	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs6667267	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs6668053	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs6670617	0.88[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap]
rs6681390	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6681618	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6681780	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs6693225	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6693423	0.83[AMR][1000 genomes]
rs727279	0.83[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs7512930	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs7521870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7523263	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs7523460	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs7537517	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs7548540	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs7552830	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs7555067	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs972361	0.88[CEU][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv872553	chr1:174195629-174373379	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1795045	chr1:174273004-174346276	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv872555	chr1:174343705-174565720	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10912773	MRPS14	cis	parietal	SCAN
rs10912773	GPR52	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174298000-174361800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:174310600-174362400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:174315600-174366400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:174318800-174369800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:174319200-174362600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:174322400-174363000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:174325800-174382800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:174326400-174346800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:174327400-174362000	Weak transcription	Primary T cells from cord blood	blood
10	chr1:174327600-174362200	Weak transcription	Aorta	Aorta
11	chr1:174328600-174343800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:174328600-174345600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:174328800-174347200	Weak transcription	Fetal Intestine Small	intestine
14	chr1:174328800-174366400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:174334800-174361800	Weak transcription	Left Ventricle	heart
16	chr1:174335000-174349600	Weak transcription	Pancreas	Pancrea
17	chr1:174335000-174361800	Weak transcription	Primary B cells from cord blood	blood
18	chr1:174339000-174345000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:174339400-174346600	Weak transcription	Fetal Heart	heart
20	chr1:174340200-174345200	Weak transcription	Adipose Nuclei	Adipose
21	chr1:174340400-174347000	Weak transcription	Thymus	Thymus
22	chr1:174341200-174353400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:174341800-174344000	Strong transcription	GM12878-XiMat	blood
24	chr1:174341800-174372200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:174342400-174346200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr1:174342600-174347000	Weak transcription	Dnd41	blood
27	chr1:174342800-174346600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:174343000-174344200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:174343000-174362200	Weak transcription	Primary T cells fromperipheralblood	blood

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