Variant report

Variant	rs10915886
Chromosome Location	chr1:226037887-226037888
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	MYC	chr1:226037727-226037928	K562	blood:	n/a	n/a
2	NFIC	chr1:226037488-226038174	ECC-1	luminal epithelium:	n/a	chr1:226037861-226037878 chr1:226037861-226037877
3	SPI1	chr1:226037754-226038043	K562	blood:	n/a	chr1:226037841-226037848
4	POLR2A	chr1:226037053-226038065	HL-60	blood:	n/a	n/a
5	POLR2A	chr1:226037146-226037930	MCF-7	breast:	n/a	n/a
6	SPI1	chr1:226037818-226038047	GM12878	blood:	n/a	chr1:226037841-226037848
7	MAX	chr1:226037584-226037945	K562	blood:	n/a	n/a
8	POLR2A	chr1:226037446-226038356	K562	blood:	n/a	n/a
9	POLR2A	chr1:226037357-226037936	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr1:226036570-226038131	HepG2	liver:	n/a	n/a
11	MAZ	chr1:226037767-226037967	K562	blood:	n/a	n/a
12	POLR2A	chr1:226037704-226038104	K562	blood:	n/a	n/a
13	SPI1	chr1:226037875-226038035	GM12878	blood:	n/a	n/a
14	SPI1	chr1:226037588-226038125	GM12878	blood:	n/a	chr1:226037841-226037848
15	RCOR1	chr1:226037684-226037916	K562	blood:	n/a	n/a
16	POLR2A	chr1:226037190-226037984	GM12892	blood:	n/a	n/a
17	NFIC	chr1:226037426-226038179	ECC-1	luminal epithelium:	n/a	chr1:226037861-226037878 chr1:226037861-226037877
18	SPI1	chr1:226037794-226038133	GM12891	blood:	n/a	chr1:226037841-226037848
19	POLR2A	chr1:226036408-226037908	Hela-S3	cervix:	n/a	n/a
20	NR2F2	chr1:226037669-226038163	K562	blood:	n/a	n/a
21	BCL3	chr1:226037714-226038470	A549	lung:	n/a	chr1:226037878-226037891 chr1:226037946-226037955
22	POLR2A	chr1:226029446-226038446	K562	blood:	n/a	n/a
23	POLR2A	chr1:226037147-226038397	K562	blood:	n/a	n/a
24	CBX3	chr1:226037608-226038036	K562	blood:	n/a	n/a
25	POLR2A	chr1:226037629-226037899	A549	lung:	n/a	n/a
26	POLR2A	chr1:226030670-226038260	A549	lung:	n/a	n/a
27	POLR2A	chr1:226037561-226038081	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:226036092-226037992	K562	blood:	n/a	n/a
29	POLR2A	chr1:226037669-226038137	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226036089..226038052-chr1:226109986..226111681,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242861	TF binding region
TMEM63A	TF binding region
ENSG00000143811	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10915883	0.84[YRI][hapmap];0.98[AFR][1000 genomes]
rs10915887	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915888	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915889	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915890	0.82[AFR][1000 genomes]
rs12070110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12071072	0.82[AFR][1000 genomes]
rs12071104	0.82[AFR][1000 genomes]
rs12071413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12075664	0.97[AFR][1000 genomes]
rs12077174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12078868	1.00[ASW][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap]
rs12079891	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080725	0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap]
rs12081742	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082207	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12083928	1.00[AFR][1000 genomes]
rs12084714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094548	0.84[YRI][hapmap]
rs12097377	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2292561	0.88[AFR][1000 genomes]
rs35273824	0.81[AFR][1000 genomes]
rs35684337	0.81[AFR][1000 genomes]
rs55706532	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56112955	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56325807	0.90[AFR][1000 genomes]
rs58852301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59728172	0.90[AFR][1000 genomes]
rs60132040	0.89[AFR][1000 genomes]
rs60739570	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61304305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150526	0.86[AFR][1000 genomes]
rs74150531	0.87[AMR][1000 genomes]
rs74150536	0.90[AFR][1000 genomes]
rs74150537	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150538	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150539	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10915886	PYCR2	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226013600-226052600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:226014800-226047800	Weak transcription	Psoas Muscle	Psoas
3	chr1:226016000-226051000	Weak transcription	NH-A	brain
4	chr1:226017400-226049800	Weak transcription	HUVEC	blood vessel
5	chr1:226020600-226042000	Weak transcription	Hela-S3	cervix
6	chr1:226020600-226042400	Weak transcription	HSMM	muscle
7	chr1:226023000-226039600	Weak transcription	NHDF-Ad	bronchial
8	chr1:226026800-226061600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:226029800-226050600	Strong transcription	Right Ventricle	heart
10	chr1:226030000-226040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:226030200-226039000	Genic enhancers	Brain Substantia Nigra	brain
12	chr1:226030400-226046800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:226030400-226052600	Weak transcription	HSMMtube	muscle
14	chr1:226030600-226039400	Strong transcription	Liver	Liver
15	chr1:226031800-226039600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:226032400-226039000	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr1:226033200-226039800	Genic enhancers	Brain Cingulate Gyrus	brain
18	chr1:226033600-226041600	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr1:226033600-226053000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:226033800-226038600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:226033800-226039200	Strong transcription	HepG2	liver
22	chr1:226033800-226039600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:226033800-226040400	Weak transcription	HMEC	breast
24	chr1:226033800-226041000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:226033800-226067400	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr1:226034000-226038000	Strong transcription	Esophagus	oesophagus
27	chr1:226034000-226039200	Strong transcription	Stomach Smooth Muscle	stomach
28	chr1:226034000-226056800	Strong transcription	Adipose Nuclei	Adipose
29	chr1:226034000-226063000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:226034200-226038000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:226034200-226039600	Weak transcription	Ovary	ovary
32	chr1:226034200-226039800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr1:226034200-226040800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:226034200-226062800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:226034600-226047600	Weak transcription	NHEK	skin
36	chr1:226034800-226040600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:226035200-226038600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr1:226035200-226039200	Genic enhancers	Fetal Lung	lung
39	chr1:226035200-226039800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:226035400-226038000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:226035400-226038200	Genic enhancers	Fetal Muscle Leg	muscle
42	chr1:226035400-226038200	Genic enhancers	Spleen	Spleen
43	chr1:226035600-226038400	Genic enhancers	K562	blood
44	chr1:226035800-226038000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr1:226035800-226039600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:226036000-226038200	Genic enhancers	Primary T cells from cord blood	blood
47	chr1:226036000-226039600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:226036000-226039600	Weak transcription	Fetal Kidney	kidney
49	chr1:226036000-226039800	Genic enhancers	Fetal Stomach	stomach
50	chr1:226036000-226040200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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