Variant report

Variant	rs10026915
Chromosome Location	chr4:57857771-57857772
allele	A/C
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	chr4:57857722-57858223	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57845155..57847188-chr4:57856587..57858696,2	MCF-7	breast:
2	chr4:57854152..57858062-chr4:57860294..57862898,3	K562	blood:
3	chr4:57856196..57858263-chr4:57863410..57864964,2	K562	blood:

Variant related genes	Relation type
ENSG00000238579	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10002090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10023009	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10034395	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11573061	0.82[CEU][hapmap]
rs11573112	0.87[YRI][hapmap]
rs11573113	0.82[ASW][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs11935933	0.88[EUR][1000 genomes]
rs11942607	0.80[EUR][1000 genomes]
rs1277296	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs13146782	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs17182939	0.82[CEU][hapmap]
rs17828496	1.00[EUR][1000 genomes]
rs1961950	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2227902	0.84[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2227903	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2271806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2271807	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[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2276896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370990	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28474684	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28520821	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28545156	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28623722	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28681160	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28719609	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3755901	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs3755904	0.82[ASW][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs3775083	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs41344750	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55734441	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56798906	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6554404	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs6837593	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs6843415	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73242618	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73242619	0.97[EUR][1000 genomes]
rs73242620	1.00[EUR][1000 genomes]
rs73242621	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73242622	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73242623	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73242625	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73242632	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7654665	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs7673980	0.94[EUR][1000 genomes]

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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv1799567	chr4:57853485-57857771	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10026915	DNASE1L2	trans	brain	seeQTL
rs10026915	TCAP	trans	brain	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846000-57881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:57846200-57861600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:57846200-57861800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:57846600-57861200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:57847000-57861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:57848000-57861400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:57848400-57860800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:57848400-57875200	Weak transcription	Stomach Mucosa	stomach
10	chr4:57848600-57900000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:57849000-57900000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:57849200-57869000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr4:57849200-57886200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:57849600-57884600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:57849800-57861400	Weak transcription	Psoas Muscle	Psoas
16	chr4:57850400-57858200	Strong transcription	Primary B cells from cord blood	blood
17	chr4:57850400-57858600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:57850600-57870200	Strong transcription	GM12878-XiMat	blood
19	chr4:57850600-57899400	Strong transcription	Fetal Thymus	thymus
20	chr4:57850800-57859400	Strong transcription	Fetal Stomach	stomach
21	chr4:57850800-57899400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:57851000-57860600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:57851000-57861200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:57851000-57899200	Strong transcription	Primary T cells from cord blood	blood
25	chr4:57851000-57899400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr4:57851200-57858400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:57851200-57859200	Strong transcription	Fetal Muscle Leg	muscle
28	chr4:57851200-57897200	Strong transcription	Fetal Intestine Large	intestine
29	chr4:57851400-57858200	Strong transcription	Thymus	Thymus
30	chr4:57851400-57894800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:57851600-57859400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:57851600-57859800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr4:57851600-57861400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:57851600-57861400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:57851600-57864400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr4:57851600-57899400	Strong transcription	Placenta	Placenta
37	chr4:57851800-57857800	Strong transcription	Brain Anterior Caudate	brain
38	chr4:57851800-57858000	Strong transcription	Colon Smooth Muscle	Colon
39	chr4:57851800-57858000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr4:57851800-57858200	Strong transcription	NHLF	lung
41	chr4:57851800-57858200	Strong transcription	Osteobl	bone
42	chr4:57851800-57858600	Strong transcription	Dnd41	blood
43	chr4:57851800-57859200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:57851800-57859800	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr4:57851800-57861200	Strong transcription	HUVEC	blood vessel
46	chr4:57851800-57861400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:57851800-57861400	Strong transcription	Adipose Nuclei	Adipose
48	chr4:57851800-57863400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr4:57851800-57868600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr4:57851800-57899400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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