Variant report

Variant	rs954884
Chromosome Location	chr12:40632958-40632959
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	chr12:40616874..40619503-chr12:40632557..40634590,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225342	Chromatin interaction
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10459265	0.81[CHB][hapmap]
rs10467146	0.85[CHB][hapmap]
rs10735934	0.85[CHB][hapmap]
rs10748014	0.85[JPT][hapmap]
rs10784444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784461	0.95[CHB][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs10784462	0.91[CHB][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs10784470	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784522	0.82[CHB][hapmap]
rs10784548	0.85[CHB][hapmap]
rs10878245	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878249	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10878262	0.98[ASN][1000 genomes]
rs10878405	0.91[CHB][hapmap]
rs10878441	0.85[CHB][hapmap]
rs11175656	0.85[JPT][hapmap]
rs11175769	0.95[CHB][hapmap];0.88[YRI][hapmap];0.88[ASN][1000 genomes]
rs11175775	0.85[ASN][1000 genomes]
rs11175784	0.90[CHB][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs11175787	0.87[ASN][1000 genomes]
rs11175836	0.86[ASN][1000 genomes]
rs11175845	0.91[CHB][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs11175847	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs11175862	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs11175911	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs11175922	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs11176030	0.82[CHB][hapmap]
rs11564148	0.82[CHB][hapmap]
rs12146857	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs12367542	0.82[CHB][hapmap]
rs12369882	0.91[CHB][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs12371502	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12426362	0.81[CHB][hapmap]
rs12820920	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs1491938	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17443815	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs17444124	0.86[CHB][hapmap]
rs17466605	0.81[CHB][hapmap]
rs17519846	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs2404580	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2404581	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2638245	0.84[JPT][hapmap]
rs2708494	0.84[JPT][hapmap]
rs3761863	0.85[CHB][hapmap]
rs3886747	0.81[CHB][hapmap]
rs4272849	0.86[CHB][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs4293189	0.86[CHB][hapmap];0.88[YRI][hapmap];0.88[ASN][1000 genomes]
rs4767973	0.81[CHB][hapmap]
rs4768230	0.86[CHB][hapmap]
rs4768236	0.85[CHB][hapmap]
rs4768237	0.81[CHB][hapmap]
rs6581667	0.81[CHB][hapmap]
rs7132171	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7302841	0.81[CHB][hapmap]
rs7309197	0.91[CHB][hapmap];0.84[YRI][hapmap];0.87[ASN][1000 genomes]
rs732374	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7955902	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7957754	0.91[CHB][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs7962011	0.82[ASN][1000 genomes]
rs7973058	0.82[CHB][hapmap]
rs7973479	0.86[CHB][hapmap];0.83[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	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	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	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
4	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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40619400-40634600	Weak transcription	Spleen	Spleen
2	chr12:40619400-40644400	Weak transcription	Gastric	stomach
3	chr12:40619600-40636400	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
6	chr12:40619800-40658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:40620400-40644200	Weak transcription	Brain Angular Gyrus	brain
8	chr12:40620800-40634800	Weak transcription	Lung	lung
9	chr12:40620800-40634800	Weak transcription	Pancreas	Pancrea
10	chr12:40620800-40644200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:40620800-40648000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:40620800-40659200	Weak transcription	Brain Anterior Caudate	brain
13	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
14	chr12:40621000-40643800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:40621000-40659800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:40621000-40661200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:40622800-40661000	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
19	chr12:40629200-40633400	Strong transcription	Adipose Nuclei	Adipose
20	chr12:40629200-40635600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:40630600-40633000	Weak transcription	Aorta	Aorta
22	chr12:40630600-40633000	Weak transcription	Ovary	ovary
23	chr12:40630600-40643600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:40630600-40669400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:40630600-40686400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:40631000-40633200	Enhancers	Hela-S3	cervix
27	chr12:40631200-40633000	Weak transcription	Liver	Liver
28	chr12:40631200-40646600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:40631400-40633200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr12:40631600-40636200	Weak transcription	NHLF	lung
31	chr12:40632000-40655200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:40632000-40656000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:40632400-40633200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:40632400-40635200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:40632600-40635200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:40632600-40635400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:40632600-40635400	Weak transcription	A549	lung
38	chr12:40632600-40635800	Weak transcription	Osteobl	bone
39	chr12:40632800-40634200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr12:40632800-40634400	Strong transcription	Primary B cells from cord blood	blood
41	chr12:40632800-40635400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:40632800-40635600	Weak transcription	NHDF-Ad	bronchial

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