Variant report

Variant	rs10488270
Chromosome Location	chr7:83770348-83770349
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:83766680..83768990-chr7:83769908..83771879,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10230974	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10231580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs10232605	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10244779	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10257628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10263183	1.00[CEU][hapmap];0.93[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10277194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10278542	0.93[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10282129	0.98[EUR][1000 genomes]
rs10488271	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11769574	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11773308	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12707621	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13222995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13228652	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13246393	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1541410	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17158648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17158650	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17158668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17158671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17301441	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2040873	0.83[EUR][1000 genomes]
rs2040874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2158567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2189851	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2214665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301892	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2372034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527031	0.87[GIH][hapmap]
rs2527035	1.00[GIH][hapmap];0.87[MEX][hapmap]
rs2691699	0.87[MEX][hapmap]
rs34018474	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34443324	0.93[ASN][1000 genomes]
rs34449541	0.93[ASN][1000 genomes]
rs34805696	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35789545	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3801653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3801656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4461845	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6959163	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7778244	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780521	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7781126	0.88[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7791361	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801600	1.00[GIH][hapmap]
rs7811829	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv888629	chr7:83722691-83896025	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1017884	chr7:83724138-83972995	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538995	chr7:83724138-83972995	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10488270	SLC25A40	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83753800-83770800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:83754000-83772200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:83754000-83774200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:83761000-83775200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:83764200-83771800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:83764400-83771000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:83764400-83774000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:83765600-83773400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:83767000-83776800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:83768000-83772000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:83768600-83770600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:83768800-83774200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:83769000-83772000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:83769000-83772200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:83769000-83772400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:83769000-83774000	Weak transcription	Colon Smooth Muscle	Colon
17	chr7:83769400-83770400	Enhancers	HepG2	liver
18	chr7:83769400-83770800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:83769400-83770800	Enhancers	NHDF-Ad	bronchial
20	chr7:83769600-83770600	Enhancers	A549	lung
21	chr7:83769600-83771000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:83769600-83771800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:83769600-83774000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:83769800-83773000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:83769800-83775200	Weak transcription	Fetal Lung	lung
26	chr7:83769800-83775200	Weak transcription	NHLF	lung
27	chr7:83769800-83775400	Weak transcription	Fetal Stomach	stomach
28	chr7:83770000-83770400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:83770000-83771400	Weak transcription	HUVEC	blood vessel
30	chr7:83770000-83771800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:83770000-83772000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr7:83770000-83774000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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