Variant report

Variant	rs10175143
Chromosome Location	chr2:112845395-112845396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr2:112844533-112845538	GM10847	blood:	n/a	n/a
2	IRF3	chr2:112844901-112845416	GM12878	blood:	n/a	n/a
3	RELA	chr2:112844392-112845519	GM19099	blood:	n/a	n/a
4	MTA3	chr2:112844678-112845411	GM12878	blood:	n/a	n/a
5	USF2	chr2:112845362-112845476	HepG2	liver:	n/a	n/a
6	RELA	chr2:112844475-112845407	GM19193	blood:	n/a	n/a
7	RELA	chr2:112844064-112845823	GM12891	blood:	n/a	n/a
8	BHLHE40	chr2:112844851-112845666	GM12878	blood:	n/a	n/a
9	RUNX3	chr2:112844728-112845431	GM12878	blood:	n/a	n/a
10	YY1	chr2:112844839-112845488	GM12892	blood:	n/a	n/a
11	RUNX3	chr2:112844781-112845456	GM12878	blood:	n/a	n/a
12	RELA	chr2:112844413-112845408	GM12878	blood:	n/a	n/a
13	MTA3	chr2:112844684-112845444	GM12878	blood:	n/a	n/a
14	MAX	chr2:112845061-112845432	GM12878	blood:	n/a	n/a
15	STAT1	chr2:112845027-112845524	GM12878	blood:	n/a	n/a
16	RELA	chr2:112844621-112845618	GM18951	blood:	n/a	n/a
17	RELA	chr2:112844729-112845415	GM12892	blood:	n/a	n/a
18	PML	chr2:112844786-112845475	GM12878	blood:	n/a	n/a
19	RELA	chr2:112844756-112845477	GM15510	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:112845353..112847041-chr2:112850152..112852401,3	K562	blood:
2	chr2:112812746..112814811-chr2:112844433..112846774,2	MCF-7	breast:
3	chr2:112841714..112844039-chr2:112844165..112846368,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM87B	TF binding region
ENSG00000153214	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10165845	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178449	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182333	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045300	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779884	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864898	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675437	0.82[AMR][1000 genomes]
rs12618637	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4241121	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257409	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4613287	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4848993	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849007	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849044	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707397	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6730057	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731563	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737707	0.86[CHD][hapmap]
rs7577442	0.97[ASN][1000 genomes]
rs7580507	1.00[ASN][1000 genomes]
rs7581849	0.90[JPT][hapmap]
rs7591702	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595574	0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308669	0.92[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653401	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10175143	CCDC138	cis	cerebellum	SCAN
rs10175143	FBLN7	cis	cerebellum	SCAN
rs10175143	POLR1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112814200-112849800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:112814200-112859800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:112816600-112866200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:112816800-112871400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:112820400-112847000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:112821400-112849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:112822200-112854400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:112822800-112876800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:112829600-112850400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:112831000-112849600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:112831800-112850800	Strong transcription	Placenta	Placenta
12	chr2:112832000-112866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:112833600-112855800	Weak transcription	Hela-S3	cervix
14	chr2:112833800-112849600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:112834600-112871200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:112834800-112849200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:112834800-112852200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:112835200-112849000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:112835200-112851000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:112835200-112851000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:112835200-112852200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:112835600-112850600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:112835800-112849400	Strong transcription	HSMM	muscle
24	chr2:112835800-112883200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:112836000-112848400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:112836000-112874400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:112838000-112849200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:112838000-112850400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:112838200-112845600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:112838200-112846600	Strong transcription	HUVEC	blood vessel
31	chr2:112838200-112847600	Strong transcription	Primary hematopoietic stem cells	blood
32	chr2:112838200-112847600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:112838200-112847800	Strong transcription	HMEC	breast
34	chr2:112838200-112848200	Strong transcription	Osteobl	bone
35	chr2:112838200-112848600	Strong transcription	NH-A	brain
36	chr2:112838200-112851200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:112838200-112851200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:112838200-112851400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:112838200-112866200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:112838200-112866400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr2:112838400-112847800	Strong transcription	NHEK	skin
42	chr2:112838400-112849200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:112838400-112849600	Strong transcription	NHDF-Ad	bronchial
44	chr2:112838400-112850200	Strong transcription	Dnd41	blood
45	chr2:112838400-112850400	Strong transcription	Liver	Liver
46	chr2:112838600-112850400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:112838600-112852200	Strong transcription	Primary T cells from cord blood	blood
48	chr2:112838600-112858200	Strong transcription	Fetal Intestine Large	intestine
49	chr2:112838800-112846200	Strong transcription	Colon Smooth Muscle	Colon
50	chr2:112838800-112847800	Strong transcription	Stomach Smooth Muscle	stomach

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