Variant report

Variant	rs10015634
Chromosome Location	chr4:57362827-57362828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57349742..57352662-chr4:57361184..57363397,2	K562	blood:
2	chr4:57344872..57347241-chr4:57362443..57365516,3	K562	blood:
3	chr4:57356189..57358476-chr4:57362362..57364129,2	K562	blood:
4	chr4:57353455..57355932-chr4:57360077..57362846,3	MCF-7	breast:
5	chr4:57343541..57346949-chr4:57360480..57364224,4	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10007967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10009543	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10015221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10866433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11610	1.00[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11733474	0.89[JPT][hapmap]
rs12648503	0.93[EUR][1000 genomes]
rs13114104	0.88[JPT][hapmap]
rs13147824	0.89[JPT][hapmap]
rs1401912	0.89[JPT][hapmap]
rs17051687	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap]
rs17086793	0.87[EUR][1000 genomes]
rs17086803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086883	0.93[EUR][1000 genomes]
rs17086887	0.93[EUR][1000 genomes]
rs2049087	0.87[GIH][hapmap];0.94[JPT][hapmap]
rs2139512	0.84[JPT][hapmap]
rs28472763	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899063	0.89[JPT][hapmap]
rs3796547	0.89[JPT][hapmap]
rs3822003	0.84[JPT][hapmap]
rs4073691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4167	0.89[JPT][hapmap]
rs4270628	0.81[CHD][hapmap]
rs4305581	0.94[JPT][hapmap]
rs4615235	0.88[EUR][1000 genomes]
rs4865102	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4865104	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4865110	0.93[EUR][1000 genomes]
rs57523479	0.93[EUR][1000 genomes]
rs58975286	0.93[ASN][1000 genomes]
rs6554355	0.89[JPT][hapmap]
rs6554356	0.89[JPT][hapmap]
rs66599079	0.93[EUR][1000 genomes]
rs68101565	0.93[EUR][1000 genomes]
rs6811482	0.93[EUR][1000 genomes]
rs6811821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6816218	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819534	0.81[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs6820417	0.88[EUR][1000 genomes]
rs6826795	0.89[JPT][hapmap]
rs6832168	0.87[EUR][1000 genomes]
rs6843587	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6848187	1.00[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs7670198	0.91[EUR][1000 genomes]
rs7683781	0.89[JPT][hapmap]
rs7692073	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7694047	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7700034	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312675	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9683679	0.89[JPT][hapmap]
rs9684298	0.89[JPT][hapmap]
rs9996593	0.87[GIH][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	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
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10015634	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs10015634	PAICS	cis	cerebellum	SCAN
rs10015634	AASDH	cis	cerebellum	SCAN
rs10015634	SRP72	cis	normal skin	skin_eQTL
rs10015634	PPAT	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
3	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:57335800-57365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:57336000-57364200	Strong transcription	Osteobl	bone
10	chr4:57336000-57369400	Strong transcription	Liver	Liver
11	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:57336200-57365000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr4:57336200-57369200	Strong transcription	Fetal Thymus	thymus
18	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
19	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:57336400-57364800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:57336400-57365400	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:57336400-57368200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr4:57336400-57369200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:57336400-57369200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:57336600-57364200	Strong transcription	Dnd41	blood
27	chr4:57336600-57365400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:57336600-57369200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:57337200-57363800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr4:57337200-57365400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:57337200-57369200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:57337600-57364000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr4:57337600-57364800	Strong transcription	Fetal Intestine Large	intestine
34	chr4:57337800-57363200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr4:57337800-57365600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:57337800-57369200	Strong transcription	Adipose Nuclei	Adipose
37	chr4:57337800-57369400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:57338000-57365000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:57338200-57364200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:57340600-57366600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:57340800-57369000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:57342000-57370200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr4:57342400-57370800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr4:57342400-57371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:57343200-57364200	Strong transcription	NH-A	brain
46	chr4:57346000-57371400	Weak transcription	Pancreas	Pancrea
47	chr4:57346600-57363200	Strong transcription	HUVEC	blood vessel
48	chr4:57347000-57365600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:57347400-57363200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:57347400-57363800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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