Variant report

Variant	rs11715248
Chromosome Location	chr3:140671286-140671287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr3:140671145-140672526	K562	blood:	n/a	chr3:140672221-140672235 chr3:140671555-140671568 chr3:140671555-140671568 chr3:140671646-140671660 chr3:140671555-140671569 chr3:140671977-140671986
2	ZNF384	chr3:140671218-140671358	K562	blood:	n/a	n/a
3	TBL1XR1	chr3:140671175-140672229	K562	blood:	n/a	n/a
4	POLR2A	chr3:140671164-140673804	HepG2	liver:	n/a	n/a
5	MAFK	chr3:140671228-140671371	K562	blood:	n/a	n/a
6	SETDB1	chr3:140671168-140672142	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:140661553..140667904-chr3:140669879..140673651,7	K562	blood:
2	chr3:140668911..140671512-chr3:140673930..140676615,2	K562	blood:
3	chr3:140670742..140673914-chr3:140680014..140683024,3	MCF-7	breast:
4	chr3:140667610..140670050-chr3:140670451..140673117,3	K562	blood:
5	chr3:140667460..140670151-chr3:140670489..140672455,2	MCF-7	breast:

Variant related genes	Relation type
SLC25A36	TF binding region
ENSG00000114120	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1047330	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs1056126	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935413	0.87[ASN][1000 genomes]
rs10935414	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs1109282	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1109283	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11707116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710204	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11710926	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711131	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713505	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713816	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs11714438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717097	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11717620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718040	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11718539	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs11718563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720342	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489397	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs13063450	0.86[ASN][1000 genomes]
rs13099706	0.86[ASN][1000 genomes]
rs1568337	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1593624	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850915	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16850917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16850926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081662	0.86[ASN][1000 genomes]
rs2292919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2311491	0.84[ASN][1000 genomes]
rs2555702	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs2555707	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2871615	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35140461	0.89[ASN][1000 genomes]
rs3755764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755765	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380393	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4524250	0.88[ASN][1000 genomes]
rs4528914	0.84[ASN][1000 genomes]
rs4538351	0.85[ASN][1000 genomes]
rs57151068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57526660	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57799705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59128309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59221985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61052022	0.92[EUR][1000 genomes]
rs61151473	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61629363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61708145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439962	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439964	0.86[ASN][1000 genomes]
rs6764740	0.84[ASN][1000 genomes]
rs6770562	0.83[ASN][1000 genomes]
rs6772634	0.86[ASN][1000 genomes]
rs6773249	0.86[ASN][1000 genomes]
rs6785007	0.89[ASN][1000 genomes]
rs6785892	0.86[ASN][1000 genomes]
rs6788711	0.86[ASN][1000 genomes]
rs6789045	0.83[ASN][1000 genomes]
rs6789116	0.84[ASN][1000 genomes]
rs6797079	0.86[ASN][1000 genomes]
rs6810200	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713354	0.81[JPT][hapmap]
rs72991025	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72991046	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7621150	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs7626525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7632043	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637899	0.85[CEU][hapmap]
rs7638206	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7643287	0.94[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs7643434	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs7643614	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs7644725	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs7649116	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs765990	0.86[ASN][1000 genomes]
rs877142	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs957093	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1005522	chr3:140454632-140685915	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536732	chr3:140454632-140685915	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh 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	10 gene(s)	inside rSNPs	diseases
4	esv1793115	chr3:140663107-140693053	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11715248	SLC25A36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140661800-140697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:140662200-140675400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:140662200-140676800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:140662200-140696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:140662400-140677000	Weak transcription	Fetal Thymus	thymus
6	chr3:140662400-140679000	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:140662400-140692200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:140662600-140672400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:140662600-140696800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:140662800-140677200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:140662800-140679200	Weak transcription	HSMMtube	muscle
12	chr3:140662800-140682200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:140662800-140695800	Weak transcription	NHLF	lung
14	chr3:140663000-140673200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:140663000-140681600	Weak transcription	NH-A	brain
16	chr3:140663200-140676400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:140663200-140692600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:140663200-140696000	Weak transcription	Fetal Stomach	stomach
19	chr3:140663400-140672600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:140663400-140697400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:140663600-140671800	Weak transcription	Hela-S3	cervix
22	chr3:140663600-140679200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:140663600-140692600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:140663800-140672800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:140664000-140672400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:140664000-140674600	Weak transcription	Right Atrium	heart
27	chr3:140664000-140676600	Weak transcription	Primary T cells from cord blood	blood
28	chr3:140664000-140679000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:140664200-140671400	Weak transcription	NHDF-Ad	bronchial
30	chr3:140664200-140671600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:140664200-140671600	Weak transcription	Osteobl	bone
32	chr3:140664200-140671800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:140664200-140676000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:140664200-140679000	Weak transcription	Primary B cells from cord blood	blood
35	chr3:140664200-140692400	Weak transcription	Fetal Brain Female	brain
36	chr3:140664200-140703800	Weak transcription	Aorta	Aorta
37	chr3:140664400-140671800	Weak transcription	HMEC	breast
38	chr3:140664400-140672800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:140664400-140679000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:140664600-140671600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:140664600-140672000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:140664600-140672000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:140664600-140672200	Weak transcription	HSMM	muscle
44	chr3:140664600-140677000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr3:140664600-140677200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:140665200-140673000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:140665400-140671400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:140665400-140698400	Weak transcription	Brain Germinal Matrix	brain
49	chr3:140665800-140672400	Weak transcription	Right Ventricle	heart
50	chr3:140665800-140672600	Weak transcription	Psoas Muscle	Psoas

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