Variant report

Variant	rs11175784
Chromosome Location	chr12:40659534-40659535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40658480..40661049-chr12:40663809..40666158,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10459265	0.90[CHB][hapmap]
rs10467146	0.89[CHB][hapmap]
rs10735934	0.89[CHB][hapmap]
rs10784444	0.90[CHB][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs10784461	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784462	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784470	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10784522	0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10784548	0.89[CHB][hapmap]
rs10878245	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs10878249	0.89[CHB][hapmap];0.89[ASN][1000 genomes]
rs10878262	0.89[ASN][1000 genomes]
rs10878405	0.95[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10878441	0.89[CHB][hapmap]
rs10878551	0.89[JPT][hapmap]
rs10878552	0.89[JPT][hapmap]
rs11175769	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175775	0.94[ASN][1000 genomes]
rs11175787	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175836	0.98[ASN][1000 genomes]
rs11175845	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175847	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175862	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11175911	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175922	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176030	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11564148	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12146857	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12311273	0.81[ASN][1000 genomes]
rs12367542	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12369882	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12371502	0.90[ASN][1000 genomes]
rs12426362	0.90[CHB][hapmap]
rs12820920	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1491938	0.95[CHB][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs17443815	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17444124	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17466605	0.90[CHB][hapmap]
rs17519846	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404580	0.95[CHB][hapmap];0.88[YRI][hapmap];0.88[ASN][1000 genomes]
rs2404581	0.86[CHB][hapmap];0.85[YRI][hapmap]
rs35124455	0.88[ASN][1000 genomes]
rs3761863	0.89[CHB][hapmap]
rs3886747	0.84[CHB][hapmap]
rs4272849	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4293189	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767973	0.90[CHB][hapmap]
rs4768230	0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4768236	0.89[CHB][hapmap]
rs4768237	0.90[CHB][hapmap]
rs6581667	0.90[CHB][hapmap]
rs6581668	0.85[CHB][hapmap]
rs7132171	0.90[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7302841	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7309197	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs732374	0.89[CHB][hapmap];0.89[ASN][1000 genomes]
rs7955902	0.89[CHB][hapmap];0.89[ASN][1000 genomes]
rs7956721	0.88[JPT][hapmap]
rs7957754	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962011	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7973058	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7973479	0.93[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs954884	0.90[CHB][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1045408	chr12:40620554-40664424	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
3	nsv1042967	chr12:40629636-40710319	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
3	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
4	chr12:40621000-40659800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:40621000-40661200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:40622800-40661000	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
8	chr12:40630600-40669400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:40630600-40686400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:40640200-40680400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
12	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
13	chr12:40641200-40662800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:40642200-40682400	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:40647600-40674000	Weak transcription	Lung	lung
16	chr12:40648800-40659800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr12:40657200-40659600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:40659000-40659600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:40659000-40659600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:40659000-40659600	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr12:40659000-40659600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr12:40659000-40659600	ZNF genes & repeats	Adipose Nuclei	Adipose
24	chr12:40659000-40659600	ZNF genes & repeats	Liver	Liver
25	chr12:40659000-40659600	ZNF genes & repeats	Psoas Muscle	Psoas
26	chr12:40659000-40659600	ZNF genes & repeats	A549	lung
27	chr12:40659000-40660600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
28	chr12:40659200-40659600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:40659200-40659600	ZNF genes & repeats	Aorta	Aorta
30	chr12:40659200-40659600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
31	chr12:40659400-40677800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:40659400-40678600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:40659400-40678600	Weak transcription	Ovary	ovary
34	chr12:40659400-40682200	Weak transcription	Brain Anterior Caudate	brain
35	chr12:40659400-40686400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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