Variant report

Variant	rs7792038
Chromosome Location	chr7:140060653-140060654
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10258709	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12665885	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12667471	0.96[MEX][hapmap]
rs12671831	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12673021	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12703771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12703772	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12703774	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12703775	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12703777	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12703778	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12703782	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12703783	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12703792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12703794	0.88[ASN][1000 genomes]
rs12703795	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12703797	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13232870	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13233309	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13244256	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3924962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4725685	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4726780	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62490396	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6953981	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6957189	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6967815	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7777207	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7778099	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9691058	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9692001	0.82[AMR][1000 genomes];0.89[EUR][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	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3391494	chr7:140060483-140064781	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7792038	SLC37A3	cis	multi-tissue	Pritchard
rs7792038	SPINT2	trans	lymphoblastoid	seeQTL
rs7792038	ZC3HAV1L	cis	parietal	SCAN
rs7792038	CREB3L2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140033600-140096000	Weak transcription	Stomach Mucosa	stomach
2	chr7:140034800-140085600	Weak transcription	Psoas Muscle	Psoas
3	chr7:140035000-140074200	Weak transcription	Right Atrium	heart
4	chr7:140038000-140061000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:140038200-140061200	Strong transcription	Fetal Stomach	stomach
6	chr7:140042000-140084800	Weak transcription	Hela-S3	cervix
7	chr7:140046000-140076200	Weak transcription	Right Ventricle	heart
8	chr7:140047600-140084200	Weak transcription	Fetal Brain Male	brain
9	chr7:140047800-140064400	Weak transcription	HMEC	breast
10	chr7:140049200-140090200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:140049600-140061200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr7:140049600-140061200	Strong transcription	Dnd41	blood
13	chr7:140049600-140067800	Weak transcription	Colon Smooth Muscle	Colon
14	chr7:140049600-140076000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:140049600-140078000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:140049600-140078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:140049600-140079400	Weak transcription	Brain Substantia Nigra	brain
18	chr7:140049800-140061000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:140050000-140061000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:140050000-140061000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr7:140050200-140061200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:140050200-140079200	Weak transcription	HUVEC	blood vessel
23	chr7:140051000-140061000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:140051400-140068400	Weak transcription	HSMM	muscle
25	chr7:140051600-140076400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr7:140052600-140075600	Weak transcription	Pancreas	Pancrea
28	chr7:140052800-140079600	Weak transcription	NHDF-Ad	bronchial
29	chr7:140054200-140079800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr7:140054600-140061200	Strong transcription	Fetal Intestine Small	intestine
31	chr7:140054600-140077800	Weak transcription	Brain Angular Gyrus	brain
32	chr7:140055000-140063400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:140055000-140063600	Weak transcription	Fetal Lung	lung
34	chr7:140055000-140068600	Weak transcription	Primary B cells from cord blood	blood
35	chr7:140055000-140068600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:140055000-140077800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr7:140055600-140067400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr7:140055600-140079200	Weak transcription	Fetal Kidney	kidney
39	chr7:140056600-140061200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:140056800-140077400	Weak transcription	NH-A	brain
41	chr7:140056800-140079400	Weak transcription	Colonic Mucosa	Colon
42	chr7:140057200-140067400	Weak transcription	HSMMtube	muscle
43	chr7:140057400-140075400	Weak transcription	Osteobl	bone
44	chr7:140057600-140063600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:140057800-140061200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:140057800-140061200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:140058200-140061000	Strong transcription	Fetal Intestine Large	intestine
48	chr7:140058400-140067400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr7:140058600-140063600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:140058600-140063800	Weak transcription	Muscle Satellite Cultured Cells	--

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