Variant report

Variant	rs28693590
Chromosome Location	chr15:31195021-31195022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:31194465..31197297-chr15:31282167..31285499,3	K562	blood:
2	chr15:31194962..31197804-chr15:31219595..31222456,2	K562	blood:
3	chr15:31194360..31196709-chr15:31282391..31284386,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166912	Chromatin interaction
ENSG00000198690	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10163148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519726	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs11070678	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070718	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs1133642	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs11631543	0.80[ASN][1000 genomes]
rs11638295	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs11852466	0.83[CHB][hapmap]
rs12441318	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs12442333	0.82[CHB][hapmap]
rs12901022	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs12902792	0.92[CHB][hapmap]
rs12904967	0.92[CHB][hapmap]
rs12907055	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911881	0.92[CHB][hapmap]
rs1404468	0.92[CHB][hapmap]
rs1404469	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs1474381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1474382	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];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483675	0.92[CHB][hapmap]
rs1524876	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs16956341	0.83[CHB][hapmap]
rs16956362	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs16956366	0.83[CHB][hapmap]
rs16956414	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs16956422	0.83[CHB][hapmap]
rs17815804	0.83[CHD][hapmap]
rs1809484	0.92[CHB][hapmap]
rs1880499	0.92[CHB][hapmap]
rs1880500	0.80[ASN][1000 genomes]
rs2042613	0.92[CHB][hapmap]
rs2113945	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs2113946	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2272218	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2272219	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2293314	0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs2293319	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2293320	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2339048	0.80[ASN][1000 genomes]
rs28548813	0.80[ASN][1000 genomes]
rs28708881	0.80[ASN][1000 genomes]
rs28721380	0.80[ASN][1000 genomes]
rs2873	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs28881289	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2949566	0.80[ASN][1000 genomes]
rs2949569	0.92[CHB][hapmap]
rs2949570	0.92[CHB][hapmap]
rs2949573	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2949575	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2949576	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2949577	0.92[CHB][hapmap]
rs2949578	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2955783	0.92[CHB][hapmap]
rs2955787	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2955790	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2955791	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2955796	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs2955798	0.80[ASN][1000 genomes]
rs2959039	0.85[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs2959049	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35162264	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497908	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3743231	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3784588	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs3964705	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs4779796	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779797	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];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493358	0.83[CHB][hapmap]
rs7161812	1.00[CHB][hapmap]
rs7164939	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7165798	0.92[CHB][hapmap]
rs7167980	0.82[ASN][1000 genomes]
rs7169064	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170710	0.92[CHB][hapmap]
rs7175951	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7176351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7182143	0.92[CHB][hapmap]
rs798101	0.85[CHB][hapmap]
rs8040345	0.92[CHB][hapmap]
rs8040989	0.92[CHB][hapmap]
rs8041717	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs871312	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs872843	0.83[CHB][hapmap]
rs9806159	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28693590	RP11-932O9.7	cis	Muscle Skeletal	GTEx
rs28693590	SNORD115-35	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31132800-31195600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:31187000-31195400	Weak transcription	NH-A	brain
3	chr15:31187000-31195600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:31194000-31195600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:31194200-31195400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:31194400-31195400	Enhancers	HepG2	liver
7	chr15:31194600-31195400	Enhancers	Thymus	Thymus
8	chr15:31194800-31195200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr15:31194800-31195400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr15:31194800-31195400	Enhancers	GM12878-XiMat	blood
11	chr15:31195000-31195200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr15:31195000-31195200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:31195000-31195200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:31195000-31195400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr15:31195000-31195400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:31195000-31195400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr15:31195000-31195400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:31195000-31195400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:31195000-31195400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:31195000-31195400	Enhancers	Brain Cingulate Gyrus	brain
21	chr15:31195000-31195400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr15:31195000-31195400	Enhancers	Fetal Brain Female	brain
23	chr15:31195000-31195400	Enhancers	Placenta	Placenta
24	chr15:31195000-31195400	Enhancers	Fetal Thymus	thymus
25	chr15:31195000-31195400	Enhancers	Gastric	stomach
26	chr15:31195000-31195400	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr15:31195000-31195600	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr15:31195000-31195600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr15:31195000-31195600	Enhancers	Pancreas	Pancrea
30	chr15:31195000-31195800	Flanking Active TSS	Dnd41	blood
31	chr15:31195000-31196600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:31195000-31196600	Active TSS	A549	lung
33	chr15:31195000-31196800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:31195000-31196800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr15:31195000-31196800	Active TSS	Rectal Smooth Muscle	rectum

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