Variant report

Variant	rs12143942
Chromosome Location	chr1:179866605-179866606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:179866560-179866631	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179851104..179853394-chr1:179865735..179868796,3	K562	blood:
2	chr1:179849456..179851628-chr1:179866576..179869234,2	MCF-7	breast:
3	chr1:179864333..179868046-chr1:179868350..179872629,6	K562	blood:
4	chr1:179849812..179857746-chr1:179862462..179868266,11	K562	blood:
5	chr1:179866194..179868046-chr1:179871129..179873011,2	K562	blood:
6	chr1:179864493..179866934-chr1:180134864..180137550,2	MCF-7	breast:
7	chr1:179864635..179867471-chr1:179879505..179882177,2	K562	blood:
8	chr1:179864202..179867093-chr1:179867105..179870142,3	K562	blood:

No data

Variant related genes	Relation type
RN7SL230P	TF binding region
ENSG00000264916	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1048418	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10494523	1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10913893	1.00[CHB][hapmap]
rs10913894	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10913895	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10913905	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913909	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11590974	1.00[CHB][hapmap]
rs12119431	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12121694	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12126625	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12136091	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136465	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142457	1.00[CHB][hapmap]
rs12144991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723969	1.00[CHB][hapmap]
rs12756362	1.00[CHB][hapmap]
rs16854910	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370139	1.00[CHB][hapmap]
rs3845388	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61740391	0.94[EUR][1000 genomes]
rs6425596	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6659939	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6673144	0.89[CEU][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72708661	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72708662	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518566	1.00[CHB][hapmap]
rs7527215	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7531195	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7545581	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7549317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9726605	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
2	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
3	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
8	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
10	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
11	chr1:179854200-179871800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:179855600-179871600	Weak transcription	A549	lung
13	chr1:179856200-179876800	Weak transcription	NHLF	lung
14	chr1:179857600-179867400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:179857600-179870000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:179857600-179871600	Weak transcription	HSMM	muscle
17	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
18	chr1:179858200-179867200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:179860000-179869800	Weak transcription	Hela-S3	cervix
20	chr1:179860000-179873800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:179860200-179890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:179860400-179871600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:179860400-179873000	Weak transcription	HUVEC	blood vessel
24	chr1:179860400-179873200	Weak transcription	K562	blood
25	chr1:179860400-179878800	Weak transcription	Colonic Mucosa	Colon
26	chr1:179860600-179869400	Weak transcription	HMEC	breast
27	chr1:179860600-179871600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:179861000-179871400	Weak transcription	NHEK	skin
29	chr1:179861000-179871600	Weak transcription	Brain Substantia Nigra	brain
30	chr1:179861200-179866800	Weak transcription	Small Intestine	intestine
31	chr1:179861200-179868400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:179861200-179869600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:179861200-179870000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:179861200-179870800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:179861200-179871400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:179861200-179878000	Weak transcription	Gastric	stomach
37	chr1:179861200-179886600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr1:179861400-179866800	Weak transcription	Stomach Mucosa	stomach
39	chr1:179861400-179869400	Weak transcription	GM12878-XiMat	blood
40	chr1:179861400-179870400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:179861400-179871000	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:179861400-179871600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:179861400-179871600	Weak transcription	Aorta	Aorta
44	chr1:179861400-179871600	Weak transcription	HSMMtube	muscle
45	chr1:179861400-179882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:179861600-179869000	Weak transcription	Primary T cells from cord blood	blood
47	chr1:179861600-179869200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:179861600-179871400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:179861600-179871600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:179861600-179871600	Weak transcription	Thymus	Thymus

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