Variant report

Variant	rs2873
Chromosome Location	chr15:31231255-31231256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31229079..31231720-chr15:31282287..31284074,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166912	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10153041	0.86[CHB][hapmap]
rs10163148	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs11070678	0.92[CHB][hapmap]
rs11070718	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs1133642	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11631543	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11638295	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs12439664	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12440244	0.86[CHB][hapmap]
rs12441318	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs12441324	0.86[CHB][hapmap]
rs12898883	0.86[CHB][hapmap]
rs12901022	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12902792	0.84[CHB][hapmap]
rs12911057	0.85[CHB][hapmap]
rs12914438	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1404468	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1404469	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1404470	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1425291	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1474381	0.92[CHB][hapmap]
rs1474382	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs1524876	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1880499	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2042613	1.00[CHB][hapmap]
rs2113945	0.92[CHB][hapmap]
rs2113946	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs2272218	0.92[CHB][hapmap]
rs2272219	0.92[CHB][hapmap]
rs2293314	0.92[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2293319	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs2293320	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2338276	0.86[CHB][hapmap]
rs2339048	0.82[ASN][1000 genomes]
rs28564430	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28693590	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs28881289	0.85[ASN][1000 genomes]
rs2949566	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2949567	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2949569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2949570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2949571	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2949573	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2949574	0.91[TSI][hapmap]
rs2949575	0.92[CHB][hapmap]
rs2949576	0.92[CHB][hapmap]
rs2949577	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2949578	0.92[CHB][hapmap]
rs2955776	0.89[EUR][1000 genomes]
rs2955783	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2955787	0.92[CHB][hapmap]
rs2955790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2955791	0.92[CHB][hapmap]
rs2955794	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2955795	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955796	0.92[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2955798	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2959039	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2959049	0.92[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2959054	0.91[TSI][hapmap]
rs35497908	0.85[ASN][1000 genomes]
rs35528291	0.86[CHB][hapmap]
rs3743231	0.92[CHB][hapmap]
rs3743233	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3794594	0.85[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs3964705	0.84[CHB][hapmap]
rs4779794	0.81[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4779796	0.92[CHB][hapmap]
rs4779797	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs7161812	0.92[CHB][hapmap]
rs7165798	1.00[CHB][hapmap]
rs7169064	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs7170710	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7175951	0.92[CHB][hapmap]
rs7176351	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs7178375	0.92[CHB][hapmap]
rs7178533	0.92[CHB][hapmap]
rs7182143	1.00[CHB][hapmap]
rs798088	0.86[CHB][hapmap]
rs798101	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs8040989	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs8041717	0.92[CHB][hapmap]
rs811768	0.86[CHB][hapmap]
rs964925	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs9806159	0.92[CHB][hapmap];0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv533434	chr15:30938215-31244225	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
7	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
10	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1039037	chr15:31140415-31277268	Strong transcription ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv542309	chr15:31140415-31277268	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv521842	chr15:31140700-31272670	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv903834	chr15:31179534-31293774	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2873	KIAA1018	cis	multi-tissue	Pritchard
rs2873	SNORD116-4	cis	parietal	SCAN
rs2873	RP11-540B6.3	cis	lung	GTEx
rs2873	MTMR10	cis	multi-tissue	Pritchard
rs2873	MTMR10	cis	Liver	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31200400-31242200	Strong transcription	Primary T cells from cord blood	blood
2	chr15:31200600-31254800	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr15:31201200-31241400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:31215200-31238600	Weak transcription	Fetal Heart	heart
5	chr15:31215200-31241000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:31215800-31236600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:31216000-31241600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:31216600-31245800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:31220000-31233800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:31221000-31246800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:31222600-31241000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:31222800-31232600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:31222800-31233000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:31223000-31232400	Weak transcription	Stomach Mucosa	stomach
15	chr15:31223200-31232400	Weak transcription	Esophagus	oesophagus
16	chr15:31223200-31237600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:31223800-31239200	Weak transcription	Fetal Brain Male	brain
18	chr15:31225400-31246200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr15:31225400-31255800	Strong transcription	Fetal Intestine Large	intestine
20	chr15:31225600-31241000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:31225600-31246000	Strong transcription	Placenta	Placenta
22	chr15:31225600-31246200	Strong transcription	Adipose Nuclei	Adipose
23	chr15:31225600-31253800	Strong transcription	Dnd41	blood
24	chr15:31225800-31241400	Strong transcription	Fetal Muscle Leg	muscle
25	chr15:31225800-31245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:31225800-31246200	Strong transcription	GM12878-XiMat	blood
27	chr15:31225800-31256000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:31226000-31241400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:31226000-31245400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:31226000-31246000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:31226000-31255800	Strong transcription	Fetal Stomach	stomach
32	chr15:31226000-31258800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr15:31226200-31232200	Strong transcription	Liver	Liver
34	chr15:31226200-31236400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:31226200-31237200	Strong transcription	Fetal Lung	lung
36	chr15:31226200-31246400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:31226200-31246800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:31226200-31269200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:31226400-31241400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:31226400-31260800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr15:31226600-31232400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:31226600-31236000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:31226600-31245400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:31226600-31246000	Strong transcription	Ovary	ovary
45	chr15:31226600-31254400	Strong transcription	Fetal Thymus	thymus
46	chr15:31226600-31255200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:31226800-31244200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr15:31226800-31245600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr15:31227000-31269600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr15:31227200-31236200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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