Variant report

Variant	rs2585110
Chromosome Location	chr15:57352893-57352894
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	FOS	chr15:57352873-57353438	MCF10A-Er-Src	breast:	n/a	chr15:57353003-57353012
2	FOSL2	chr15:57352779-57353561	SK-N-SH	brain:	n/a	chr15:57353003-57353012
3	POLR2A	chr15:57352852-57353413	SK-N-SH	brain:	n/a	n/a
4	FOSL1	chr15:57352846-57353560	HCT-116	colon:	n/a	chr15:57353003-57353012
5	RXRA	chr15:57352818-57353430	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr15:57352659-57353585	SK-N-SH	brain:	n/a	n/a
7	GATA2	chr15:57352786-57353361	HUVEC	blood vessel:	n/a	n/a
8	YY1	chr15:57352642-57353228	SK-N-SH	brain:	n/a	chr15:57352768-57352776 chr15:57352763-57352782 chr15:57352765-57352775
9	FOS	chr15:57352743-57353426	HUVEC	blood vessel:	n/a	chr15:57353003-57353012
10	PBX3	chr15:57352726-57353583	SK-N-SH	brain:	n/a	n/a
11	FOSL2	chr15:57352864-57353442	A549	lung:	n/a	chr15:57353003-57353012
12	TCF12	chr15:57352752-57353604	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr15:57352796-57353523	HUVEC	blood vessel:	n/a	n/a
14	PBX3	chr15:57352805-57353506	SK-N-SH	brain:	n/a	n/a
15	STAT3	chr15:57352787-57353138	MCF10A-Er-Src	breast:	n/a	n/a
16	TCF12	chr15:57352619-57353647	SK-N-SH	brain:	n/a	n/a
17	FOXA1	chr15:57352818-57353241	HepG2	liver:	n/a	n/a
18	JUND	chr15:57352795-57353594	SK-N-SH	brain:	n/a	chr15:57353003-57353012
19	NFIC	chr15:57352622-57353603	SK-N-SH	brain:	n/a	n/a
20	SP1	chr15:57352872-57353409	HCT-116	colon:	n/a	n/a
21	EP300	chr15:57352749-57353630	SK-N-SH	brain:	n/a	chr15:57353001-57353015 chr15:57353005-57353014
22	TEAD4	chr15:57352745-57353513	SK-N-SH	brain:	n/a	n/a
23	EP300	chr15:57352801-57353685	SK-N-SH	brain:	n/a	chr15:57353001-57353015 chr15:57353005-57353014
24	MAFK	chr15:57352748-57353343	IMR90	lung:	n/a	n/a
25	JUND	chr15:57352809-57353596	SK-N-SH	brain:	n/a	chr15:57353003-57353012
26	GATA3	chr15:57352688-57353608	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57352117..57354489-chr15:57357081..57359694,2	K562	blood:
2	chr15:57352117..57354569-chr15:57356374..57360031,3	K562	blood:

Variant related genes	Relation type
TCF12	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1020888	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap]
rs12437753	0.84[AMR][1000 genomes]
rs12437777	0.93[AMR][1000 genomes]
rs12438464	0.93[AMR][1000 genomes]
rs12439010	0.93[AMR][1000 genomes]
rs12439149	0.90[AMR][1000 genomes]
rs12439165	0.90[AMR][1000 genomes]
rs12439547	0.87[AMR][1000 genomes]
rs12439994	0.90[AMR][1000 genomes]
rs12440790	0.90[AMR][1000 genomes]
rs12441185	0.90[MEX][hapmap];0.93[AMR][1000 genomes]
rs12441200	0.90[AMR][1000 genomes]
rs12441263	0.90[AMR][1000 genomes]
rs12441888	0.93[AMR][1000 genomes]
rs12441892	0.93[AMR][1000 genomes]
rs12442238	0.90[AMR][1000 genomes]
rs12442326	0.93[AMR][1000 genomes]
rs1542508	1.00[YRI][hapmap]
rs1642932	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap]
rs1652734	0.81[ASN][1000 genomes]
rs1652735	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1652736	1.00[CHB][hapmap]
rs16977246	1.00[CHB][hapmap];0.95[YRI][hapmap]
rs16977269	0.95[YRI][hapmap]
rs17238971	0.84[AMR][1000 genomes]
rs17238992	0.90[AMR][1000 genomes]
rs17239020	0.93[AMR][1000 genomes]
rs17239047	0.93[AMR][1000 genomes]
rs17239068	0.93[AMR][1000 genomes]
rs17239089	0.93[AMR][1000 genomes]
rs17819694	0.90[AMR][1000 genomes]
rs17819755	0.93[AMR][1000 genomes]
rs17819779	0.92[AMR][1000 genomes]
rs17819809	0.93[AMR][1000 genomes]
rs17819839	0.92[AMR][1000 genomes]
rs1816322	0.92[AMR][1000 genomes]
rs1841692	0.95[YRI][hapmap]
rs2011551	0.88[YRI][hapmap]
rs2116064	0.89[YRI][hapmap]
rs213146	0.81[YRI][hapmap]
rs213150	0.82[CEU][hapmap]
rs2576928	1.00[CHD][hapmap]
rs2585084	0.87[MKK][hapmap];0.88[YRI][hapmap];0.80[ASN][1000 genomes]
rs2585118	0.84[YRI][hapmap]
rs2593230	0.87[CHD][hapmap]
rs2615233	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2703587	1.00[CHB][hapmap]
rs2703589	1.00[CHB][hapmap]
rs2703620	1.00[CHB][hapmap]
rs2733194	0.91[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs2733195	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2733339	0.91[ASW][hapmap];1.00[CHB][hapmap];0.95[MKK][hapmap];0.90[YRI][hapmap]
rs4494480	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4774911	0.88[YRI][hapmap]
rs57813422	0.81[ASN][1000 genomes]
rs604191	1.00[ASW][hapmap];1.00[CHD][hapmap];0.85[MKK][hapmap]
rs6493904	0.94[YRI][hapmap]
rs7161894	0.89[YRI][hapmap]
rs7164557	0.94[YRI][hapmap]
rs7175983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs7180911	0.95[YRI][hapmap]
rs73413325	0.87[ASN][1000 genomes]
rs73413333	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73413352	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs74018485	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs8025829	0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs8037469	0.91[ASW][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs8040557	0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2585110	PRTG	cis	parietal	SCAN
rs2585110	GALNT9	trans	lymphoblastoid	seeQTL
rs2585110	AQP9	cis	cerebellum	SCAN
rs2585110	TMOD2	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
2	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:57328200-57353600	Weak transcription	Pancreas	Pancrea
4	chr15:57328600-57355000	Weak transcription	Dnd41	blood
5	chr15:57332000-57355800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr15:57336600-57371800	Weak transcription	K562	blood
7	chr15:57339600-57355600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:57339800-57361600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr15:57343800-57363400	Weak transcription	Aorta	Aorta
11	chr15:57344600-57363600	Weak transcription	Right Atrium	heart
12	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:57346600-57355000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:57347000-57373400	Weak transcription	Fetal Intestine Small	intestine
15	chr15:57347200-57356200	Weak transcription	Fetal Kidney	kidney
16	chr15:57347600-57373000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:57347600-57373200	Weak transcription	Fetal Intestine Large	intestine
18	chr15:57348200-57361800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:57348600-57356800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:57348800-57355000	Enhancers	Osteobl	bone
21	chr15:57349000-57354400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:57349200-57353800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:57349200-57355400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:57349200-57356600	Enhancers	Brain Substantia Nigra	brain
25	chr15:57349600-57359800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:57349800-57357800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:57349800-57363800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:57349800-57366600	Weak transcription	Psoas Muscle	Psoas
29	chr15:57350000-57353800	Enhancers	HSMM	muscle
30	chr15:57350000-57355000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:57350200-57353000	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:57350200-57360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:57350200-57363800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:57350400-57353000	Weak transcription	Fetal Thymus	thymus
35	chr15:57350400-57355200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:57350400-57356000	Enhancers	HUVEC	blood vessel
37	chr15:57350400-57362400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr15:57350400-57372400	Weak transcription	Fetal Lung	lung
39	chr15:57350400-57373400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr15:57350400-57374000	Weak transcription	Ovary	ovary
41	chr15:57350600-57353400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr15:57350600-57355400	Enhancers	NHEK	skin
43	chr15:57350800-57356200	Weak transcription	Fetal Heart	heart
44	chr15:57351000-57353200	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr15:57351000-57354600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:57351000-57354600	Enhancers	NH-A	brain
47	chr15:57351000-57356400	Enhancers	HMEC	breast
48	chr15:57351200-57353800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:57351200-57354200	Enhancers	NHDF-Ad	bronchial
50	chr15:57351200-57356800	Enhancers	Brain Cingulate Gyrus	brain

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