Variant report

Variant	rs2469542
Chromosome Location	chr15:76557476-76557477
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	POLR2A	chr15:76555475-76558482	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76548818..76551250-chr15:76556678..76559451,2	MCF-7	breast:

Variant related genes	Relation type
TYRO3P	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11072576	0.89[CHB][hapmap]
rs11072579	0.85[CHB][hapmap]
rs11072580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072583	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs11072585	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs11072587	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs11634060	0.85[CHB][hapmap]
rs11636851	0.85[CHB][hapmap]
rs12050896	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs12438741	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12439484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12440815	0.80[EUR][1000 genomes]
rs12442266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12592171	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs12592501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12595211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12595717	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[EUR][1000 genomes]
rs12595738	0.96[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs12898415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12899871	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs12901160	0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12902506	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12907668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12907805	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs12908334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12911035	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12913096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916022	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1474117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16968083	0.85[CHB][hapmap]
rs17361504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17362383	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs17460201	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs1850722	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs1875888	0.84[CHB][hapmap]
rs2117369	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs2139190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2176623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404974	0.82[ASN][1000 genomes]
rs2456045	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2456046	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2456050	0.84[CHB][hapmap]
rs2460141	0.84[YRI][hapmap]
rs2460154	0.96[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2469208	0.81[YRI][hapmap]
rs2469541	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2469548	0.84[CHB][hapmap]
rs2469565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469566	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs284895	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs2959850	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2959853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34213321	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34893715	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35707798	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784449	0.83[CHB][hapmap]
rs3866543	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs3898352	0.85[CHB][hapmap]
rs4079681	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs4381566	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4633676	0.88[JPT][hapmap]
rs4886484	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4886485	0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4886488	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs4886777	0.84[CHB][hapmap]
rs4886783	0.84[CHB][hapmap]
rs4886787	0.85[CHB][hapmap]
rs4886788	0.85[CHB][hapmap]
rs4886789	0.84[CHB][hapmap]
rs4886791	0.84[CHB][hapmap]
rs4886799	0.88[JPT][hapmap]
rs4886801	0.88[JPT][hapmap]
rs55805818	0.80[ASN][1000 genomes]
rs67418609	0.80[EUR][1000 genomes]
rs7164060	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs7164813	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs7174889	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7177923	0.85[CHB][hapmap]
rs7179142	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs7180462	0.84[CHB][hapmap]
rs7403276	0.88[JPT][hapmap]
rs8028504	0.84[CHB][hapmap]
rs8029637	0.84[CHB][hapmap]
rs8030411	0.88[JPT][hapmap]
rs8030454	0.85[CHB][hapmap]
rs8033494	0.84[CHB][hapmap]
rs8039545	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs869452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs870295	0.84[CHB][hapmap]
rs879625	0.85[CHB][hapmap]
rs883993	0.84[CHB][hapmap]
rs937732	0.89[CHB][hapmap]
rs937733	0.85[CHB][hapmap]
rs959991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv527608	chr15:76530267-76562738	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76513200-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:76517400-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:76546800-76558200	Weak transcription	Brain Angular Gyrus	brain
4	chr15:76550400-76563000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:76550600-76559200	ZNF genes & repeats	Fetal Stomach	stomach
6	chr15:76550600-76560400	ZNF genes & repeats	Fetal Intestine Large	intestine
7	chr15:76550600-76562600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
8	chr15:76550600-76563000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr15:76550600-76563200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:76550600-76563400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:76550600-76563400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:76550600-76563600	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr15:76550600-76564000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr15:76550600-76578400	Strong transcription	Liver	Liver
15	chr15:76552000-76559400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:76553200-76558800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr15:76553400-76562800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:76553400-76563200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
19	chr15:76553600-76560800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
20	chr15:76553600-76561000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr15:76553600-76563200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:76553800-76558200	ZNF genes & repeats	Fetal Brain Female	brain
23	chr15:76553800-76562600	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr15:76553800-76564200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:76554000-76560200	Weak transcription	Gastric	stomach
26	chr15:76554000-76560400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
27	chr15:76554000-76563800	ZNF genes & repeats	Dnd41	blood
28	chr15:76554200-76561600	ZNF genes & repeats	Fetal Muscle Leg	muscle
29	chr15:76554200-76562600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr15:76554200-76562600	ZNF genes & repeats	Fetal Lung	lung
31	chr15:76554400-76557600	ZNF genes & repeats	Fetal Heart	heart
32	chr15:76554600-76560600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
33	chr15:76554600-76563000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
34	chr15:76555000-76557600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:76555000-76557600	ZNF genes & repeats	Thymus	Thymus
36	chr15:76555000-76557600	ZNF genes & repeats	NH-A	brain
37	chr15:76555000-76557800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:76555000-76557800	Strong transcription	Rectal Smooth Muscle	rectum
39	chr15:76555000-76558000	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr15:76555000-76558200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
41	chr15:76555000-76558200	ZNF genes & repeats	K562	blood
42	chr15:76555000-76558400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:76555000-76559200	ZNF genes & repeats	Placenta	Placenta
44	chr15:76555000-76560600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
45	chr15:76555000-76562600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:76555000-76563200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:76555200-76557600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
48	chr15:76555200-76557600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
49	chr15:76555200-76557800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:76555200-76557800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon

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