Variant report

Variant	rs1150954
Chromosome Location	chr12:31679036-31679037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:31612968..31613587-chr12:31678930..31679823,2	MCF-7	breast:
2	chr12:31612637..31613514-chr12:31678906..31679710,3	MCF-7	breast:
3	chr12:31612782..31613587-chr12:31678930..31679828,6	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1012154	0.81[CEU][hapmap];0.92[CHB][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10771832	0.86[CHB][hapmap]
rs10843947	0.86[CHB][hapmap]
rs11051418	0.85[CHB][hapmap]
rs11051456	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1150942	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150943	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150945	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150950	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1150953	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1150955	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150963	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615961	0.86[CHB][hapmap]
rs1259233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259235	0.90[CEU][hapmap];0.92[CHB][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1259241	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259352	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1259353	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259354	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1259389	0.85[ASN][1000 genomes]
rs1259395	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1259405	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1259422	0.88[AFR][1000 genomes]
rs1259426	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259430	0.84[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1259432	0.86[AMR][1000 genomes]
rs1259435	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259438	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259441	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1262390	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1271128	0.86[AMR][1000 genomes]
rs1271663	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1272773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469673	0.86[CHB][hapmap]
rs1542536	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1677154	0.85[AFR][1000 genomes]
rs1677186	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1677187	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1677189	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1677217	0.80[EUR][1000 genomes]
rs1716194	0.82[ASN][1000 genomes]
rs1716216	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2061761	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2116704	0.86[CHB][hapmap]
rs2374190	0.94[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs2568884	0.92[CHB][hapmap]
rs2568885	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568887	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2568888	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2568894	0.84[AMR][1000 genomes]
rs2568902	0.90[AMR][1000 genomes]
rs2604052	0.91[ASN][1000 genomes]
rs2617178	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617191	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2617200	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2682671	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682674	0.86[ASN][1000 genomes]
rs2682677	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682679	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682680	0.89[ASN][1000 genomes]
rs2682686	0.84[EUR][1000 genomes]
rs2682695	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682697	0.83[CHB][hapmap]
rs3898368	0.86[CHB][hapmap]
rs4312145	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs708200	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs708209	0.86[CHB][hapmap]
rs708212	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs708215	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs708217	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7294574	0.86[CHB][hapmap]
rs7302698	0.86[CHB][hapmap]
rs792871	0.94[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs792875	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793148	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793149	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793150	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793158	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793161	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793171	0.90[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793173	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793175	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793176	0.92[CHB][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs793177	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793191	0.95[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs7959877	0.86[CHB][hapmap]
rs7962896	0.86[CHB][hapmap]
rs7975761	0.86[CHB][hapmap]
rs7976644	0.86[CHB][hapmap]
rs899159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs976874	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31667800-31687600	Weak transcription	Pancreas	Pancrea
2	chr12:31671000-31680200	Weak transcription	Right Atrium	heart
3	chr12:31672200-31680000	Weak transcription	Right Ventricle	heart
4	chr12:31672800-31681000	Weak transcription	Brain Anterior Caudate	brain
5	chr12:31673000-31684600	Weak transcription	Aorta	Aorta
6	chr12:31673000-31685200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:31673200-31679600	Weak transcription	Brain Substantia Nigra	brain
8	chr12:31673400-31681200	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:31673400-31681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:31673400-31688400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:31675600-31689000	Weak transcription	Small Intestine	intestine
12	chr12:31675800-31679200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:31676000-31681000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:31676000-31685800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:31676400-31679200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:31676400-31684600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:31676800-31679200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:31676800-31681000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:31677000-31683600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:31677000-31683600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:31677000-31684000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:31677200-31679600	Enhancers	Primary B cells from peripheral blood	blood
23	chr12:31677200-31680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:31677200-31681000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:31677200-31683600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:31677600-31679600	Flanking Active TSS	GM12878-XiMat	blood
27	chr12:31677600-31680200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:31677600-31680400	Enhancers	Brain Angular Gyrus	brain
29	chr12:31677600-31681600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:31677800-31679400	Enhancers	Primary B cells from cord blood	blood
31	chr12:31677800-31679800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:31677800-31680200	Enhancers	Fetal Kidney	kidney
33	chr12:31677800-31680200	Enhancers	Hela-S3	cervix
34	chr12:31677800-31683600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:31678000-31686400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:31678200-31681000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:31678200-31686400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:31678400-31680400	Enhancers	Adipose Nuclei	Adipose
39	chr12:31678400-31680400	Enhancers	HepG2	liver
40	chr12:31678600-31679600	Enhancers	Fetal Intestine Small	intestine
41	chr12:31678600-31679600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:31678600-31680400	Enhancers	Ovary	ovary
43	chr12:31678600-31681400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:31678600-31683600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:31678800-31679200	Active TSS	A549	lung
46	chr12:31678800-31679800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:31678800-31684600	Weak transcription	HSMM	muscle
48	chr12:31679000-31679400	Weak transcription	Fetal Heart	heart
49	chr12:31679000-31679600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:31679000-31680000	Enhancers	Liver	Liver

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