Variant report

Variant	rs11187968
Chromosome Location	chr10:96227430-96227431
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96160655..96163170-chr10:96227233..96229998,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108239	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10882476	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11187933	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11187953	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11187969	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11187971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11187974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11187994	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11188000	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11188001	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11527882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11528075	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12220941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2265045	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2764379	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs495896	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7093613	0.82[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs7901625	0.90[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][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	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11187968	ENTPD1	cis	parietal	SCAN
rs11187968	SCARNA3	trans	lymphoblastoid	seeQTL
rs11187968	ALDH18A1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96190800-96234600	Weak transcription	Osteobl	bone
2	chr10:96203000-96239600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr10:96203400-96242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:96204200-96243400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:96210200-96248800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr10:96211600-96292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:96212600-96248600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:96213000-96234400	Weak transcription	HSMM	muscle
9	chr10:96215600-96255200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr10:96216600-96243600	Weak transcription	Brain Anterior Caudate	brain
11	chr10:96218800-96235000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr10:96219800-96235200	Weak transcription	Left Ventricle	heart
13	chr10:96219800-96239600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:96219800-96242800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:96219800-96283400	Weak transcription	Lung	lung
16	chr10:96220000-96248800	Weak transcription	Colonic Mucosa	Colon
17	chr10:96220600-96234200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr10:96221800-96238000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:96221800-96255600	Weak transcription	Ovary	ovary
20	chr10:96222200-96237200	Weak transcription	Liver	Liver
21	chr10:96222800-96255800	Weak transcription	HepG2	liver
22	chr10:96223200-96293600	Weak transcription	NHDF-Ad	bronchial
23	chr10:96223400-96231800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:96223400-96237600	Weak transcription	Fetal Intestine Small	intestine
25	chr10:96223400-96240200	Weak transcription	Brain Hippocampus Middle	brain
26	chr10:96223600-96237200	Weak transcription	Fetal Lung	lung
27	chr10:96223600-96242600	Weak transcription	Fetal Muscle Leg	muscle
28	chr10:96224000-96234600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr10:96224400-96237400	Weak transcription	Fetal Stomach	stomach
30	chr10:96227400-96227800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:96227400-96228000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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