Variant report

Variant	rs2404974
Chromosome Location	chr15:76556699-76556700
allele	G/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
2	POLR2A	chr15:76556699-76556716	HUVEC	blood vessel:	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: 97 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11072576	0.87[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072577	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072578	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072579	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072583	0.96[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072585	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072587	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11629459	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11631690	0.81[EUR][1000 genomes]
rs11631764	0.82[EUR][1000 genomes]
rs11631874	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11633405	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634060	0.91[CEU][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634472	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634796	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11636278	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11636851	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637855	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12050896	0.96[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438741	0.80[ASN][1000 genomes]
rs12442266	0.80[ASN][1000 genomes]
rs12443449	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12898415	0.80[ASN][1000 genomes]
rs12913096	0.82[ASN][1000 genomes]
rs16968083	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1850722	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1875888	0.91[CEU][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2007928	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2016734	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2056251	0.81[ASN][1000 genomes]
rs2176623	0.80[ASN][1000 genomes]
rs2456049	0.81[ASN][1000 genomes]
rs2456050	0.87[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2456057	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2456071	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2469210	0.90[ASN][1000 genomes]
rs2469542	0.82[ASN][1000 genomes]
rs2469548	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2938697	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35707798	0.80[ASN][1000 genomes]
rs35831705	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784449	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3898352	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3915459	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3915460	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3927264	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3958426	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3991792	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3991793	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3991794	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4592616	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886486	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886487	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886488	0.86[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886777	0.87[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886779	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886781	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886783	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886784	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886787	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886788	0.96[CEU][hapmap]
rs4886789	0.96[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886791	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5012144	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55794488	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55805818	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56737606	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57182285	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60017340	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60290059	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60371615	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60561507	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61018254	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61275737	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61300240	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62027018	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62027047	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62027048	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62030232	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62030245	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62030246	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495197	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7177923	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7179750	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7180462	0.96[CEU][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8028504	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8029637	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8030454	0.87[CEU][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8033494	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8039063	0.91[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs870295	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs879625	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs883993	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs937732	0.91[CEU][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs937733	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2404974	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2404974	ISL2	cis	Whole Blood	GTEx
rs2404974	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2404974	SCAPER	cis	Thyroid	GTEx
rs2404974	SCAPER	cis	lung	GTEx
rs2404974	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2404974	SCAPER	cis	Whole Blood	GTEx

Chromatin state (count:112 , 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	chr15:76550600-76557400	Strong transcription	Stomach Smooth Muscle	stomach
6	chr15:76550600-76559200	ZNF genes & repeats	Fetal Stomach	stomach
7	chr15:76550600-76560400	ZNF genes & repeats	Fetal Intestine Large	intestine
8	chr15:76550600-76562600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
9	chr15:76550600-76563000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr15:76550600-76563200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:76550600-76563400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:76550600-76563400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:76550600-76563600	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr15:76550600-76564000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr15:76550600-76578400	Strong transcription	Liver	Liver
16	chr15:76552000-76559400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:76553200-76558800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr15:76553400-76562800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:76553400-76563200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
20	chr15:76553600-76560800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
21	chr15:76553600-76561000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr15:76553600-76563200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:76553800-76556800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
24	chr15:76553800-76558200	ZNF genes & repeats	Fetal Brain Female	brain
25	chr15:76553800-76562600	ZNF genes & repeats	Primary B cells from cord blood	blood
26	chr15:76553800-76564200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:76554000-76560200	Weak transcription	Gastric	stomach
28	chr15:76554000-76560400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
29	chr15:76554000-76563800	ZNF genes & repeats	Dnd41	blood
30	chr15:76554200-76561600	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr15:76554200-76562600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
32	chr15:76554200-76562600	ZNF genes & repeats	Fetal Lung	lung
33	chr15:76554400-76557600	ZNF genes & repeats	Fetal Heart	heart
34	chr15:76554600-76557000	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
35	chr15:76554600-76557400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
36	chr15:76554600-76560600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
37	chr15:76554600-76563000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
38	chr15:76555000-76557000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:76555000-76557600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:76555000-76557600	ZNF genes & repeats	Thymus	Thymus
41	chr15:76555000-76557600	ZNF genes & repeats	NH-A	brain
42	chr15:76555000-76557800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:76555000-76557800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr15:76555000-76558000	ZNF genes & repeats	Brain Germinal Matrix	brain
45	chr15:76555000-76558200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
46	chr15:76555000-76558200	ZNF genes & repeats	K562	blood
47	chr15:76555000-76558400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:76555000-76559200	ZNF genes & repeats	Placenta	Placenta
49	chr15:76555000-76560600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr15:76555000-76562600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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