Variant report

Variant	rs9787880
Chromosome Location	chr11:36312762-36312763
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:36311774..36314121-chr11:36530055..36531908,2	K562	blood:
2	chr11:36309810..36312786-chr11:36530434..36531939,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175104	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10836528	0.86[YRI][hapmap]
rs10836531	0.80[MKK][hapmap]
rs11033524	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11033527	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11602024	0.91[AFR][1000 genomes]
rs11603166	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12361221	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1562327	0.81[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs17814690	0.86[YRI][hapmap]
rs1900336	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289986	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2289987	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4418777	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56386213	0.86[AFR][1000 genomes]
rs61878683	0.87[AFR][1000 genomes]
rs61878687	0.92[EUR][1000 genomes]
rs6484831	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7104737	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7107433	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7109505	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72946165	0.90[AFR][1000 genomes]
rs7951298	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9667667	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9787894	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888212	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9888261	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9787880	SLC1A2	cis	parietal	SCAN
rs9787880	LINC00610	cis	Thyroid	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36311400-36313800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:36311400-36314000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:36311400-36314000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:36311400-36314000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:36311400-36317400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:36311400-36322600	Weak transcription	Spleen	Spleen
7	chr11:36311400-36331400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:36311600-36312800	Enhancers	Brain Hippocampus Middle	brain
9	chr11:36311600-36312800	Enhancers	Brain Substantia Nigra	brain
10	chr11:36311600-36313800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr11:36311600-36313800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:36311600-36313800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:36311600-36314000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr11:36311600-36314000	Weak transcription	Adipose Nuclei	Adipose
15	chr11:36311600-36314200	Weak transcription	Fetal Intestine Small	intestine
16	chr11:36311600-36317000	Weak transcription	Hela-S3	cervix
17	chr11:36311600-36317400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:36311600-36317600	Weak transcription	Fetal Intestine Large	intestine
19	chr11:36311600-36318400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr11:36311600-36318600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:36311600-36325800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:36311800-36313800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:36311800-36317200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:36311800-36321800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:36312000-36316600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr11:36312200-36313200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:36312200-36317800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:36312400-36312800	Enhancers	Stomach Mucosa	stomach
29	chr11:36312400-36314000	Weak transcription	Brain Anterior Caudate	brain
30	chr11:36312600-36312800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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