Variant report

Variant	rs1259236
Chromosome Location	chr12:31624800-31624801
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	chr12:31623959..31626445-chr12:31627744..31630687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256159	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1012154	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10743757	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10743758	0.84[CEU][hapmap];0.93[CHB][hapmap]
rs10771832	0.84[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap]
rs10843947	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs11051418	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs11051437	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11051441	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1150953	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11615961	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1259235	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1259428	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs1259432	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1469673	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1716216	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2116704	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2568884	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2617190	1.00[JPT][hapmap]
rs2617200	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2682697	1.00[JPT][hapmap]
rs3844573	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs3850965	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3898368	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4482118	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4931501	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4931507	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6487992	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs708209	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7133082	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7135856	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7136476	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs7294574	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7302698	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7307616	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7313118	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs793176	0.86[CHB][hapmap]
rs7954595	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7957026	0.84[CEU][hapmap]
rs7959877	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7962896	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7974437	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7975761	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7976644	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]

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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31542400-31645000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:31562400-31644400	Weak transcription	Brain Substantia Nigra	brain
3	chr12:31567400-31635800	Weak transcription	Osteobl	bone
4	chr12:31567800-31642800	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:31572000-31631200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:31572000-31631200	Weak transcription	HSMMtube	muscle
7	chr12:31572400-31627400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:31572400-31628400	Weak transcription	Right Ventricle	heart
9	chr12:31572400-31631200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:31577800-31649400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:31579000-31632000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:31579400-31626400	Weak transcription	Left Ventricle	heart
13	chr12:31579400-31632000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:31585000-31631600	Weak transcription	Brain Anterior Caudate	brain
16	chr12:31585000-31642000	Weak transcription	Fetal Kidney	kidney
17	chr12:31585400-31631800	Weak transcription	Fetal Lung	lung
18	chr12:31586200-31635800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:31594400-31648400	Weak transcription	Small Intestine	intestine
20	chr12:31600200-31626400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:31600600-31630400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:31600600-31632000	Weak transcription	Brain Germinal Matrix	brain
23	chr12:31600800-31631600	Weak transcription	Adipose Nuclei	Adipose
24	chr12:31603800-31632600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:31605400-31630800	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:31605400-31631200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:31605400-31647200	Weak transcription	Psoas Muscle	Psoas
28	chr12:31605600-31632000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:31605600-31632200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:31605600-31637000	Weak transcription	Fetal Stomach	stomach
31	chr12:31607400-31631200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:31608600-31632000	Weak transcription	Placenta	Placenta
33	chr12:31610200-31632000	Weak transcription	Ovary	ovary
34	chr12:31613400-31627400	Weak transcription	Fetal Intestine Large	intestine
35	chr12:31613400-31631200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:31613400-31632000	Weak transcription	HSMM	muscle
37	chr12:31613600-31626200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:31613600-31629400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:31615400-31632000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:31618200-31632200	Weak transcription	Aorta	Aorta
41	chr12:31619000-31632200	Weak transcription	Fetal Brain Female	brain
42	chr12:31619600-31635800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:31620000-31631200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:31620000-31635600	Weak transcription	HUVEC	blood vessel
45	chr12:31620200-31644800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:31620600-31626800	Weak transcription	HepG2	liver
47	chr12:31620600-31631400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:31621400-31626600	Strong transcription	Fetal Intestine Small	intestine
49	chr12:31622400-31628600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:31622800-31629000	Weak transcription	GM12878-XiMat	blood

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