Variant report

Variant	rs2949578
Chromosome Location	chr15:31272995-31272996
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:31267165..31269336-chr15:31272115..31274886,2	K562	blood:
2	chr15:31271252..31273468-chr15:31279975..31283092,3	K562	blood:
3	chr15:31269911..31273536-chr15:31281736..31285109,4	MCF-7	breast:
4	chr15:31272157..31276720-chr15:31281759..31286309,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166912	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10163148	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10519726	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs11070678	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070718	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs1133642	0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs11638295	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs12437580	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439664	0.82[ASN][1000 genomes]
rs12441318	0.85[CHB][hapmap]
rs12442333	0.82[CHB][hapmap]
rs12443369	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12901022	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs12906480	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914207	0.84[ASN][1000 genomes]
rs12914438	0.82[ASN][1000 genomes]
rs1404467	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1404468	0.92[CHB][hapmap]
rs1404469	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs1404470	0.82[ASN][1000 genomes]
rs1425291	0.82[ASN][1000 genomes]
rs1474381	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1474382	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1524876	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs16956341	0.83[CHB][hapmap]
rs16956362	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs16956366	0.83[CHB][hapmap]
rs16956414	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs16956422	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs17815804	0.88[CHD][hapmap]
rs1880499	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2042613	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2113945	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs2113946	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2140735	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2272218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293319	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2293320	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2339048	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28693590	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2873	0.92[CHB][hapmap]
rs2949568	0.82[GIH][hapmap];0.91[TSI][hapmap]
rs2949569	0.92[CHB][hapmap];0.84[CHD][hapmap]
rs2949570	0.92[CHB][hapmap]
rs2949572	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2949573	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2949575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2949576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2949577	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2955783	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2955787	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2955790	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2955791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2955796	0.85[CHB][hapmap]
rs2959039	0.85[CHB][hapmap]
rs2959047	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2959049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2959050	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2959051	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3743231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784588	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs4344701	0.81[ASN][1000 genomes]
rs4779796	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4779797	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6493358	0.83[CHB][hapmap]
rs71474640	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7161812	1.00[CHB][hapmap]
rs7164530	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7164939	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7165798	0.92[CHB][hapmap]
rs7169064	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7170710	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs7170772	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7175256	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7175951	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176351	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7178375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7178533	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7182143	0.92[CHB][hapmap]
rs7183880	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798101	0.85[CHB][hapmap]
rs8040989	0.92[CHB][hapmap]
rs8041717	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs871312	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs872843	0.83[CHB][hapmap]
rs964925	0.84[CHD][hapmap]
rs9806159	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
17	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2949578	MTMR10	cis	multi-tissue	Pritchard
rs2949578	RP11-932O9.7	cis	Muscle Skeletal	GTEx
rs2949578	SNORD115-35	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31242000-31282800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:31245000-31276400	Weak transcription	Brain Germinal Matrix	brain
3	chr15:31248800-31283000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:31249000-31276000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:31250200-31282200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:31250800-31282400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:31251200-31277200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:31251200-31282400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:31251600-31282200	Weak transcription	Hela-S3	cervix
10	chr15:31252800-31282400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:31254600-31276400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:31254600-31277200	Weak transcription	HSMMtube	muscle
13	chr15:31255200-31276800	Weak transcription	Fetal Brain Female	brain
14	chr15:31255600-31277000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:31255800-31277000	Weak transcription	Fetal Intestine Small	intestine
16	chr15:31255800-31277000	Weak transcription	Fetal Stomach	stomach
17	chr15:31256000-31282400	Weak transcription	Fetal Brain Male	brain
18	chr15:31258200-31277000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:31258200-31277800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:31258400-31277000	Weak transcription	Gastric	stomach
21	chr15:31258800-31273400	Weak transcription	Lung	lung
22	chr15:31259600-31274800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:31262200-31282200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:31262400-31277200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:31262400-31277200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:31264400-31274400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:31265600-31276800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:31265600-31277000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr15:31265800-31275200	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:31266000-31277000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:31266400-31278000	Weak transcription	Colonic Mucosa	Colon
32	chr15:31266600-31275000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:31266600-31277400	Weak transcription	Osteobl	bone
34	chr15:31267200-31275600	Weak transcription	GM12878-XiMat	blood
35	chr15:31267600-31274400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:31267600-31277200	Weak transcription	A549	lung
37	chr15:31267800-31273600	Weak transcription	HSMM	muscle
38	chr15:31267800-31274600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:31267800-31276200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:31267800-31276400	Weak transcription	HMEC	breast
41	chr15:31267800-31277200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:31267800-31277800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:31267800-31282000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr15:31269200-31273600	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr15:31269400-31273200	Weak transcription	NH-A	brain
46	chr15:31269400-31274000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:31269400-31275800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr15:31270000-31273000	Genic enhancers	Placenta	Placenta
49	chr15:31270000-31273400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr15:31270000-31273600	Enhancers	Brain Cingulate Gyrus	brain

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