Variant report

Variant	rs7394878
Chromosome Location	chr11:9198276-9198277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:9198183-9198297	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9197229..9199544-chr11:9481637..9484255,2	MCF-7	breast:
2	chr11:9169410..9173680-chr11:9196051..9200398,3	MCF-7	breast:

Variant related genes	Relation type
DENND5A	TF binding region
ENSG00000268403	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000184014	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10047438	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1039210	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10769991	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs10769994	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10769995	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10769996	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10769997	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10769998	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10769999	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10840183	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840185	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10840202	0.86[CHD][hapmap]
rs11042199	0.86[CHB][hapmap]
rs11042200	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042211	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11042213	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12099067	0.90[CHD][hapmap]
rs12286943	0.86[CHD][hapmap]
rs12291375	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1353730	0.81[CHD][hapmap]
rs17256375	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs1827011	0.87[MEX][hapmap]
rs1874822	0.84[CHB][hapmap]
rs2133217	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291839	0.86[CHD][hapmap]
rs2742556	0.87[MEX][hapmap]
rs4537761	0.86[CHD][hapmap]
rs56077948	0.80[ASN][1000 genomes]
rs6486199	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6486206	0.89[YRI][hapmap]
rs6486210	0.95[YRI][hapmap]
rs6486231	0.94[YRI][hapmap]
rs7103596	0.81[CHD][hapmap]
rs7109745	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7112540	0.95[YRI][hapmap]
rs7114688	0.95[YRI][hapmap]
rs7120239	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7123970	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.84[ASN][1000 genomes]
rs7395151	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7395347	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs7395846	0.82[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7396439	0.95[YRI][hapmap]
rs7396705	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7925308	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]
rs7925418	0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7930507	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7947251	0.86[CHB][hapmap]
rs956517	0.89[ASN][1000 genomes]
rs9888257	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[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	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7394878	TMEM41B	cis	multi-tissue	Pritchard
rs7394878	OR56A1	cis	cerebellum	SCAN
rs7394878	EIF4G2	cis	cerebellum	SCAN
rs7394878	TRIM5	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9155000-9203400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:9161200-9202400	Weak transcription	Small Intestine	intestine
3	chr11:9162000-9230600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:9166000-9200600	Weak transcription	Colonic Mucosa	Colon
5	chr11:9169200-9198400	Weak transcription	Thymus	Thymus
6	chr11:9169600-9238000	Weak transcription	Esophagus	oesophagus
7	chr11:9171800-9230200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:9172000-9230400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:9172200-9199600	Weak transcription	Gastric	stomach
10	chr11:9173000-9199400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:9173400-9199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:9173600-9199600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:9174000-9199400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:9174000-9225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:9180000-9199600	Weak transcription	Aorta	Aorta
16	chr11:9182400-9225000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr11:9182400-9231800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:9182600-9199000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr11:9182600-9199600	Weak transcription	Fetal Brain Male	brain
20	chr11:9184200-9208200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:9184200-9216800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:9186800-9215800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:9187600-9201800	Weak transcription	Pancreas	Pancrea
24	chr11:9190000-9198400	Weak transcription	Fetal Intestine Small	intestine
25	chr11:9191600-9198400	Weak transcription	Right Ventricle	heart
26	chr11:9191600-9199600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:9191800-9199200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr11:9191800-9199400	Weak transcription	HMEC	breast
29	chr11:9192000-9198800	Weak transcription	Colon Smooth Muscle	Colon
30	chr11:9192200-9199200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr11:9192200-9199600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr11:9192400-9198600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:9192400-9199600	Weak transcription	Spleen	Spleen
34	chr11:9193000-9198600	Weak transcription	Lung	lung
35	chr11:9193000-9199600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:9193600-9199400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr11:9193800-9202600	Weak transcription	Fetal Heart	heart
38	chr11:9194000-9203400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:9194200-9199200	Weak transcription	Psoas Muscle	Psoas
40	chr11:9195000-9199000	Weak transcription	Osteobl	bone
41	chr11:9195200-9198600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:9195200-9199400	Weak transcription	Hela-S3	cervix
43	chr11:9195200-9199400	Weak transcription	K562	blood
44	chr11:9195400-9198400	Weak transcription	Fetal Stomach	stomach
45	chr11:9195400-9199000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:9195400-9199400	Weak transcription	GM12878-XiMat	blood
47	chr11:9196200-9200400	Strong transcription	HUVEC	blood vessel
48	chr11:9196200-9203800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr11:9196400-9203200	Strong transcription	NHLF	lung
50	chr11:9196400-9204000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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