Variant report

Variant	rs2101019
Chromosome Location	chr15:59947740-59947741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59903703..59905876-chr15:59946460..59948688,2	K562	blood:
2	chr15:59947605..59950537-chr15:59979625..59981765,3	MCF-7	breast:
3	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
4	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:

Variant related genes	Relation type
ENSG00000140297	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000259238	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1002181	0.85[EUR][1000 genomes]
rs10152209	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10152414	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10152415	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10152509	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10162629	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1046053	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs1057059	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11071465	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11071468	0.85[EUR][1000 genomes]
rs11071469	0.85[EUR][1000 genomes]
rs1135148	0.91[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs11634067	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11637071	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637359	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11853610	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11854063	0.95[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12441240	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12593480	0.85[EUR][1000 genomes]
rs12708458	0.87[EUR][1000 genomes]
rs12708459	0.87[EUR][1000 genomes]
rs12902582	0.95[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12902774	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12903647	0.82[EUR][1000 genomes]
rs12906392	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907554	0.84[EUR][1000 genomes]
rs12907641	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12909005	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12912652	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1479885	0.82[EUR][1000 genomes]
rs1531638	0.84[EUR][1000 genomes]
rs1531639	0.84[EUR][1000 genomes]
rs1552031	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1871499	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1871500	0.95[CEU][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1871503	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1871504	0.84[YRI][hapmap]
rs1979422	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2170062	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2306354	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306355	0.95[CEU][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2307272	0.84[EUR][1000 genomes]
rs2307273	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2307275	0.95[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2414638	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28671744	0.86[EUR][1000 genomes]
rs2899649	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34797071	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34894301	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3825870	0.87[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4232	0.82[CEU][hapmap]
rs4270113	0.84[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4533213	0.84[EUR][1000 genomes]
rs4774340	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4774341	0.88[EUR][1000 genomes]
rs4775191	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4775195	0.95[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs4775197	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6151441	0.89[YRI][hapmap]
rs6151458	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6151460	0.84[EUR][1000 genomes]
rs6151461	0.95[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs6151462	0.95[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6151467	0.84[EUR][1000 genomes]
rs6151470	0.84[EUR][1000 genomes]
rs6151472	0.82[EUR][1000 genomes]
rs6151474	0.84[EUR][1000 genomes]
rs6151477	0.84[EUR][1000 genomes]
rs6151483	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151486	0.84[EUR][1000 genomes]
rs6151487	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151501	0.83[EUR][1000 genomes]
rs6151503	0.85[EUR][1000 genomes]
rs6151504	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs6151506	0.85[EUR][1000 genomes]
rs6151510	0.91[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151514	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6151525	0.95[CEU][hapmap];0.80[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151528	0.83[EUR][1000 genomes]
rs6151529	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6151532	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6151533	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6151535	0.91[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs6151536	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs6151542	0.85[EUR][1000 genomes]
rs6151545	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs6151551	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151553	0.95[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151557	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151561	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151565	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151568	0.95[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6151570	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151571	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6151574	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6151576	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151580	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6151581	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6151586	0.95[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151588	0.95[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151589	0.95[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151590	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151592	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62012358	0.84[EUR][1000 genomes]
rs62015260	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62015289	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6494127	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6494128	0.84[EUR][1000 genomes]
rs6494130	0.84[EUR][1000 genomes]
rs6494131	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6494133	0.86[EUR][1000 genomes]
rs67697180	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67820349	0.85[EUR][1000 genomes]
rs7162964	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs7164756	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7172270	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7173827	0.89[YRI][hapmap]
rs7178050	0.84[EUR][1000 genomes]
rs7178211	0.89[YRI][hapmap]
rs7180408	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7182962	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs722163	0.84[EUR][1000 genomes]
rs722164	0.84[EUR][1000 genomes]
rs7497974	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7882	0.84[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033161	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8035465	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8040114	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8041223	0.87[CHD][hapmap]
rs8041394	1.00[CEU][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
7	nsv1043693	chr15:59944471-59971500	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2101019	PRTG	cis	parietal	SCAN
rs2101019	GTF2A2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59925600-59948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:59926600-59948000	Weak transcription	Brain Angular Gyrus	brain
3	chr15:59927200-59948800	Weak transcription	Aorta	Aorta
4	chr15:59930600-59948200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:59932800-59947800	Weak transcription	Colonic Mucosa	Colon
6	chr15:59932800-59948000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:59936000-59948000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:59938200-59947800	Weak transcription	NHLF	lung
9	chr15:59938200-59948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:59938600-59949200	Weak transcription	Lung	lung
11	chr15:59941000-59949200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:59941200-59948000	Weak transcription	Fetal Stomach	stomach
13	chr15:59943000-59948200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:59944200-59948000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:59944200-59948200	Weak transcription	Fetal Intestine Small	intestine
16	chr15:59944400-59947800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:59944400-59947800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:59944400-59947800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:59944400-59947800	Weak transcription	HUVEC	blood vessel
20	chr15:59944400-59948000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:59944400-59948000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:59944600-59947800	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:59944600-59948000	Weak transcription	Fetal Brain Male	brain
24	chr15:59944600-59948000	Weak transcription	Fetal Brain Female	brain
25	chr15:59944600-59948000	Weak transcription	Osteobl	bone
26	chr15:59944600-59948400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:59945000-59947800	Weak transcription	HMEC	breast
28	chr15:59945000-59948000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:59945000-59948000	Weak transcription	NH-A	brain
30	chr15:59945200-59947800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:59945200-59948200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:59945400-59947800	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:59945400-59947800	Weak transcription	Placenta	Placenta
34	chr15:59945400-59948000	Weak transcription	Fetal Lung	lung
35	chr15:59945400-59948000	Weak transcription	HSMMtube	muscle
36	chr15:59945400-59948400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:59945600-59947800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:59945600-59948000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:59945600-59948000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr15:59945600-59948000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:59945600-59948000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:59945600-59948800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:59945800-59947800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:59945800-59947800	Weak transcription	Fetal Kidney	kidney
45	chr15:59946000-59948800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr15:59946200-59947800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:59946200-59948600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:59946400-59948000	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr15:59946400-59948000	Weak transcription	Thymus	Thymus
50	chr15:59946600-59948000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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