Variant report

Variant	rs10861013
Chromosome Location	chr12:103836146-103836147
allele	A/G
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	EP300	chr12:103835988-103836286	GM12878	blood:	n/a	chr12:103836086-103836100
2	CHD2	chr12:103836006-103836291	GM12878	blood:	n/a	n/a
3	SPI1	chr12:103835005-103836176	GM12878	blood:	n/a	chr12:103835561-103835570 chr12:103835559-103835572 chr12:103835558-103835571

Variant related genes	Relation type
C12orf42	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10161272	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10507166	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10735387	0.82[EUR][1000 genomes]
rs10745964	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10745965	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10778240	0.89[GIH][hapmap]
rs10778241	0.86[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10778244	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10778246	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10778253	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs10778257	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10860997	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861000	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861005	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861014	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861016	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861022	0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs10861025	0.82[EUR][1000 genomes]
rs11111555	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11111556	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11111572	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111579	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111582	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1320345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2374045	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2374056	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2374057	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2374065	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2374078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2888733	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597156	0.83[EUR][1000 genomes]
rs6539073	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7137784	0.85[EUR][1000 genomes]
rs7295887	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7298211	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7300757	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7301460	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7302890	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7303147	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304308	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7305169	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7305704	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7312095	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7313836	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7313920	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7952759	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7961410	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7967003	0.87[GIH][hapmap]
rs7967288	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7970043	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7970506	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3338592	chr12:103817534-103849094	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10861013	FAM71C	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103834400-103836200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:103834400-103836400	Enhancers	Thymus	Thymus
3	chr12:103834400-103837400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:103835000-103836400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:103835200-103836200	Enhancers	Primary hematopoietic stem cells	blood
6	chr12:103835200-103836400	Enhancers	Fetal Thymus	thymus
7	chr12:103835200-103837400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:103835400-103836400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:103835400-103836600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr12:103835400-103837400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr12:103835400-103838200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:103835600-103836600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:103835600-103836800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:103835600-103837000	Enhancers	Dnd41	blood
15	chr12:103835600-103837200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr12:103835600-103837400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:103835600-103837600	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:103835600-103837600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:103835600-103837600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr12:103835600-103837600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr12:103835600-103837800	Enhancers	Primary T cells from cord blood	blood
22	chr12:103835600-103838400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:103835600-103838400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr12:103835600-103838800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:103835800-103837400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:103835800-103837600	Enhancers	Primary B cells from cord blood	blood
27	chr12:103836000-103837200	Flanking Active TSS	GM12878-XiMat	blood

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