Variant report

Variant	rs2255663
Chromosome Location	chr15:43829008-43829009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	15:43807815-43812531..15:43825784-43834250	K562	blood:
2	15:43792489-43802874..15:43825784-43834250	K562	blood:
3	chr15:43819879..43821980-chr15:43828096..43830428,2	MCF-7	breast:
4	15:43825784-43834250..15:44067689-44069261	Hela-S3	cervix:
5	15:43825784-43834250..15:44034348-44042259	Hela-S3	cervix:
6	15:43782117-43785993..15:43825784-43834250	Hela-S3	cervix:
7	chr15:43828054..43831995-chr15:43833960..43836416,4	K562	blood:
8	chr15:43823602..43825884-chr15:43826737..43829270,3	K562	blood:

Variant related genes	Relation type
ENSG00000205771	Chromatin interaction
ENSG00000167004	Chromatin interaction
ENSG00000067369	Chromatin interaction
ENSG00000166963	Chromatin interaction
ENSG00000128886	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1060939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1079309	0.91[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12905772	0.91[CEU][hapmap]
rs1814538	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs1869258	1.00[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2242069	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs2244981	0.91[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2245715	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2249952	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2251844	0.99[ASN][1000 genomes]
rs2253268	0.91[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2253708	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2254927	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255042	1.00[ASN][1000 genomes]
rs2255051	0.96[ASN][1000 genomes]
rs2255410	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255440	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2264050	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2264876	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs2278857	0.87[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2412781	0.91[CEU][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap]
rs2439831	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2439832	0.95[JPT][hapmap]
rs2439834	0.90[ASN][1000 genomes]
rs2439839	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2439843	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439845	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2439846	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2439850	0.95[JPT][hapmap]
rs2444032	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2444244	0.95[ASN][1000 genomes]
rs2444250	0.95[JPT][hapmap]
rs2444251	0.91[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2467736	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2467737	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2467738	0.91[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2467739	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2467741	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2467742	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2467745	0.91[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470130	1.00[ASN][1000 genomes]
rs2470131	1.00[ASN][1000 genomes]
rs2584725	0.80[ASN][1000 genomes]
rs2602141	0.91[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28649346	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2915788	0.96[ASN][1000 genomes]
rs2924369	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2927070	0.80[AMR][1000 genomes]
rs2927071	0.83[MEX][hapmap];0.88[TSI][hapmap]
rs3097773	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3809482	0.91[CEU][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap]
rs4296223	0.91[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs4547312	0.87[CEU][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs475486	0.93[ASN][1000 genomes]
rs480108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486301	0.99[ASN][1000 genomes]
rs493377	0.91[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs495175	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs496584	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs506120	0.91[CEU][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs509306	0.80[EUR][1000 genomes]
rs518288	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs523156	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs529611	1.00[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs536313	0.91[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs537115	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs542898	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs548704	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs560191	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs570933	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572837	1.00[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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493083	0.91[CEU][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap]
rs689647	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs689693	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689767	0.91[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689781	0.81[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs689797	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689826	0.95[JPT][hapmap]
rs689835	0.95[JPT][hapmap]
rs689883	0.97[ASN][1000 genomes]
rs690012	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs690276	0.91[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs690316	0.91[JPT][hapmap]
rs690367	0.91[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690436	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs690446	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690466	0.95[JPT][hapmap]
rs690472	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690512	0.91[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs693510	0.91[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs694725	0.91[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs694985	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7163288	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs7497780	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9920879	0.91[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS 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 miRNA target site	101 gene(s)	inside rSNPs	diseases
3	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv437799	chr15:43784000-43989518	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv832988	chr15:43804641-43976862	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv428304	chr15:43823158-44008580	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
8	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
10	nsv428633	chr15:43823160-44008580	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2255663	STRCP1	cis	Esophagus Muscularis	GTEx
rs2255663	CEP120	cis	Liver	GTEx
rs2255663	CCDC100	trans	multi-tissue	Pritchard
rs2255663	HISPPD2A	cis	multi-tissue	Pritchard
rs2255663	STRCP1	cis	Whole Blood	GTEx
rs2255663	ZNF690	cis	multi-tissue	Pritchard
rs2255663	AC011330.5	cis	Thyroid	GTEx
rs2255663	ZSCAN29	cis	multi-tissue	Pritchard
rs2255663	MGAT1	cis	Liver	GTEx
rs2255663	ZSCAN29	cis	Thyroid	GTEx
rs2255663	TGM5	cis	multi-tissue	Pritchard
rs2255663	STRC	cis	multi-tissue	Pritchard
rs2255663	AC011330.5	cis	Artery Tibial	GTEx
rs2255663	TGM5	cis	lymphoblastoid	seeQTL
rs2255663	TRIM28	trans	multi-tissue	Pritchard
rs2255663	TRIM28	cis	Liver	GTEx
rs2255663	TGM7	cis	Esophagus Mucosa	GTEx
rs2255663	MGAT1	trans	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43811400-43829200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:43812000-43844400	Weak transcription	Fetal Brain Male	brain
3	chr15:43815400-43833600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:43815800-43839400	Weak transcription	Stomach Mucosa	stomach
5	chr15:43818000-43835400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:43818000-43852600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:43818200-43851600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:43822800-43842800	Weak transcription	HSMM	muscle
9	chr15:43823000-43830200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:43823200-43830000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:43823200-43835600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:43823600-43837400	Weak transcription	Fetal Lung	lung
13	chr15:43823600-43840000	Weak transcription	Psoas Muscle	Psoas
14	chr15:43823800-43829200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:43823800-43833200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:43823800-43836400	Weak transcription	NHLF	lung
17	chr15:43823800-43852600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr15:43824000-43830000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:43824200-43833400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:43824200-43842800	Weak transcription	HSMMtube	muscle
21	chr15:43824200-43845000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:43824400-43830000	Weak transcription	NHDF-Ad	bronchial
23	chr15:43824800-43853000	Weak transcription	GM12878-XiMat	blood
24	chr15:43824800-43853200	Weak transcription	Hela-S3	cervix
25	chr15:43825200-43830000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:43825600-43829200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:43826000-43829400	Strong transcription	Fetal Intestine Large	intestine
28	chr15:43826000-43832000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:43827200-43849800	Weak transcription	Colonic Mucosa	Colon
30	chr15:43827400-43829600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:43827400-43830800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:43827400-43831400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:43827400-43834200	Weak transcription	Fetal Brain Female	brain
34	chr15:43827400-43839800	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:43827400-43841400	Weak transcription	NHEK	skin
36	chr15:43827400-43842400	Weak transcription	Osteobl	bone
37	chr15:43827400-43852600	Weak transcription	Left Ventricle	heart
38	chr15:43827400-43854000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:43827600-43829200	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:43827600-43829400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:43827600-43829800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:43827600-43830800	Weak transcription	Fetal Intestine Small	intestine
43	chr15:43827600-43834200	Weak transcription	Dnd41	blood
44	chr15:43827600-43837000	Weak transcription	Gastric	stomach
45	chr15:43827600-43839200	Weak transcription	Primary T cells from cord blood	blood
46	chr15:43827600-43839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:43827600-43840400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:43827600-43840400	Weak transcription	Fetal Stomach	stomach
49	chr15:43827600-43846800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:43827600-43848400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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