Variant report

Variant	rs7313231
Chromosome Location	chr12:40418224-40418225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1005956	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10506140	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10747971	0.84[JPT][hapmap]
rs10784338	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10784353	0.83[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs10784356	0.83[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs10784359	0.94[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10784369	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs10877891	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10877990	0.82[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10878031	0.82[ASN][1000 genomes]
rs10878049	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10878089	0.93[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11174609	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs11174670	0.80[ASN][1000 genomes]
rs11174702	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11174809	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11174812	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174813	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175024	0.93[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12813098	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs12823555	1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1472118	0.81[YRI][hapmap]
rs1482281	0.84[JPT][hapmap]
rs1586038	0.83[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs1600866	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs1813122	0.84[JPT][hapmap]
rs2128275	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2128277	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2404352	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs2896825	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896905	0.93[ASW][hapmap];0.89[CHB][hapmap];0.80[GIH][hapmap];0.84[LWK][hapmap];0.84[YRI][hapmap]
rs3925535	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4625545	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767960	0.90[ASN][1000 genomes]
rs4768200	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4768204	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs530602	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs550669	0.84[JPT][hapmap]
rs555740	0.84[JPT][hapmap]
rs6581504	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6650226	0.84[JPT][hapmap]
rs7139216	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs716268	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7313209	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953129	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7954875	0.80[ASN][1000 genomes]
rs7959498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960662	0.92[JPT][hapmap]
rs7964150	0.84[JPT][hapmap]
rs7970812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9669240	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7313231	AC079630.2	cis	Esophagus Mucosa	GTEx
rs7313231	SLC2A13	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40402200-40425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:40405400-40445200	Weak transcription	K562	blood
4	chr12:40405800-40421000	Weak transcription	Left Ventricle	heart
5	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
7	chr12:40406000-40423200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:40406600-40423200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:40406600-40425800	Weak transcription	Liver	Liver
10	chr12:40407800-40426000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:40409600-40426000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:40410000-40422200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:40411000-40418800	Weak transcription	Aorta	Aorta
14	chr12:40411400-40428200	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:40411400-40428600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:40411600-40418800	Weak transcription	Right Atrium	heart
17	chr12:40411600-40422000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:40411600-40424000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:40411600-40425600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr12:40411600-40426200	Weak transcription	Esophagus	oesophagus
21	chr12:40411800-40425200	Weak transcription	Fetal Intestine Small	intestine
22	chr12:40411800-40425600	Weak transcription	Fetal Intestine Large	intestine
23	chr12:40411800-40425600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:40411800-40426400	Weak transcription	Right Ventricle	heart
25	chr12:40415000-40426000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:40416200-40425400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:40416600-40425400	Weak transcription	Psoas Muscle	Psoas
28	chr12:40416600-40441800	Weak transcription	Ovary	ovary
29	chr12:40417000-40426000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:40417000-40426400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:40417200-40420000	Weak transcription	Lung	lung
32	chr12:40417200-40421000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:40417200-40423000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:40417200-40425200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:40417200-40425400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:40417200-40425600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:40417400-40419200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:40417600-40419000	Enhancers	Brain Germinal Matrix	brain
39	chr12:40418200-40421000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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