Variant report

Variant	rs4909943
Chromosome Location	chr11:10670073-10670074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:10662421..10664986-chr11:10669210..10672158,2	K562	blood:
2	chr11:10655188..10657860-chr11:10668660..10671375,2	MCF-7	breast:
3	chr11:10661837..10665351-chr11:10668716..10672933,3	K562	blood:
4	chr11:10669554..10672277-chr11:10684119..10685938,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072952	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1035693	0.84[JPT][hapmap]
rs10770128	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[ASN][1000 genomes]
rs10770129	0.89[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10840451	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10840454	0.98[ASN][1000 genomes]
rs10840455	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10840456	0.89[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10840458	0.84[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap]
rs11042904	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs11042909	0.98[ASN][1000 genomes]
rs12295574	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1544863	0.91[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1559652	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2033049	0.81[ASN][1000 genomes]
rs2113897	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3993279	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[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4909944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910164	0.89[ASN][1000 genomes]
rs7108708	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs7119452	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs7127014	0.80[ASN][1000 genomes]
rs7935285	0.83[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs7938635	0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs9633862	0.84[ASN][1000 genomes]
rs9633863	0.89[ASN][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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4909943	TUB	cis	parietal	SCAN
rs4909943	GVIN1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10646000-10679000	Weak transcription	Fetal Lung	lung
2	chr11:10646200-10679200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:10650400-10678600	Weak transcription	Right Ventricle	heart
4	chr11:10651800-10670600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:10658800-10676600	Enhancers	Primary B cells from peripheral blood	blood
6	chr11:10661200-10673600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:10662400-10672000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:10663600-10670200	Weak transcription	NHDF-Ad	bronchial
9	chr11:10664200-10672000	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:10664200-10678800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:10664400-10675000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr11:10664600-10670600	Weak transcription	Primary B cells from cord blood	blood
13	chr11:10665600-10672200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:10666400-10671800	Genic enhancers	Stomach Smooth Muscle	stomach
15	chr11:10667600-10671400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:10668200-10670400	Strong transcription	Fetal Stomach	stomach
17	chr11:10668200-10671000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:10668200-10671000	Weak transcription	Ovary	ovary
19	chr11:10668200-10673200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:10668200-10673400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:10668400-10670400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:10668400-10671600	Genic enhancers	Colon Smooth Muscle	Colon
23	chr11:10668400-10672200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr11:10668400-10673200	Weak transcription	Left Ventricle	heart
25	chr11:10668400-10673800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:10668600-10670200	Weak transcription	Right Atrium	heart
27	chr11:10668600-10670800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:10668600-10671200	Enhancers	Placenta	Placenta
29	chr11:10668600-10672600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:10668600-10673400	Weak transcription	Spleen	Spleen
31	chr11:10668600-10674200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:10668600-10674400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:10668800-10670200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr11:10668800-10670200	Enhancers	K562	blood
35	chr11:10668800-10671400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr11:10668800-10672000	Weak transcription	Brain Angular Gyrus	brain
37	chr11:10668800-10673400	Weak transcription	Esophagus	oesophagus
38	chr11:10668800-10674200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr11:10669000-10671400	Weak transcription	Brain Anterior Caudate	brain
40	chr11:10669200-10672000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:10669200-10673400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:10669400-10670400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:10669400-10670400	Strong transcription	Aorta	Aorta
44	chr11:10669400-10671400	Weak transcription	Brain Hippocampus Middle	brain
45	chr11:10669400-10672000	Weak transcription	Brain Substantia Nigra	brain
46	chr11:10669400-10672000	Weak transcription	NHLF	lung
47	chr11:10669400-10673200	Weak transcription	Lung	lung
48	chr11:10669400-10673200	Weak transcription	NH-A	brain
49	chr11:10669400-10674400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:10669600-10670600	Weak transcription	Fetal Intestine Small	intestine

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