Variant report

Variant	rs7122293
Chromosome Location	chr11:9874505-9874506
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10840316	0.87[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11042519	0.95[ASN][1000 genomes]
rs12099354	0.81[AFR][1000 genomes]
rs12362504	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs12800780	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1546541	0.82[AFR][1000 genomes]
rs1546542	0.82[ASW][hapmap];0.80[LWK][hapmap];0.81[AFR][1000 genomes]
rs2017503	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35749184	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910067	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4910073	0.87[EUR][1000 genomes]
rs55813311	0.85[EUR][1000 genomes]
rs56138865	0.85[EUR][1000 genomes]
rs56981829	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60975667	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7929338	0.81[AFR][1000 genomes]
rs7942326	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7950839	0.84[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9300100	0.87[CEU][hapmap];0.87[EUR][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7122293	LMO1	cis	parietal	SCAN
rs7122293	SWAP70	cis	parietal	SCAN
rs7122293	OVCH2	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9818600-9881400	Weak transcription	Spleen	Spleen
2	chr11:9830400-9880400	Weak transcription	Thymus	Thymus
3	chr11:9830800-9880600	Weak transcription	Fetal Brain Male	brain
4	chr11:9833600-9878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:9834200-9876600	Weak transcription	Brain Germinal Matrix	brain
6	chr11:9834600-9877200	Weak transcription	Right Ventricle	heart
7	chr11:9837600-9885800	Weak transcription	Hela-S3	cervix
8	chr11:9838600-9879800	Weak transcription	Fetal Thymus	thymus
9	chr11:9848200-9877000	Weak transcription	HepG2	liver
10	chr11:9851200-9880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:9851600-9875400	Weak transcription	Stomach Mucosa	stomach
12	chr11:9851600-9880400	Weak transcription	Small Intestine	intestine
13	chr11:9853400-9877400	Weak transcription	Brain Substantia Nigra	brain
14	chr11:9854000-9877400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:9854000-9880600	Weak transcription	Colonic Mucosa	Colon
16	chr11:9856600-9880000	Weak transcription	Fetal Heart	heart
17	chr11:9859800-9880200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr11:9861400-9875400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:9861400-9877000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:9861400-9877400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:9861400-9879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:9861400-9879800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:9861400-9879800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:9861400-9880800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr11:9863000-9879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:9863200-9876800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr11:9863400-9876000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr11:9863400-9877600	Weak transcription	HMEC	breast
29	chr11:9863400-9880000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:9863600-9879800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:9863800-9883800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:9864000-9875400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr11:9865000-9879800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr11:9865800-9877200	Weak transcription	Gastric	stomach
35	chr11:9866000-9880400	Weak transcription	Esophagus	oesophagus
36	chr11:9866000-9880400	Weak transcription	Pancreas	Pancrea
37	chr11:9868400-9877200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:9868600-9876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:9868600-9876800	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:9868600-9883400	Weak transcription	HSMMtube	muscle
41	chr11:9868800-9875200	Weak transcription	Fetal Kidney	kidney
42	chr11:9868800-9876400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr11:9868800-9876800	Weak transcription	NHLF	lung
44	chr11:9868800-9877000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:9868800-9877200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:9868800-9877200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr11:9868800-9877200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:9868800-9877400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr11:9868800-9877400	Weak transcription	Brain Angular Gyrus	brain
50	chr11:9868800-9879800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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