Variant report

Variant	rs1129406
Chromosome Location	chr12:51203371-51203372
allele	C/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	GATA1	chr12:51202900-51203422	PBDE	blood:	n/a	n/a
2	ZNF384	chr12:51202992-51203492	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51156449..51158602-chr12:51202622..51204712,2	K562	blood:
2	chr12:51202962..51206871-chr12:51207911..51210941,4	K562	blood:
3	chr12:51159281..51161379-chr12:51202424..51204535,2	K562	blood:

Variant related genes	Relation type
ENSG00000271490	TF binding region
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10783387	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876084	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876087	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876092	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876098	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169506	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs11169524	0.89[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs11169562	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169563	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169570	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169571	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169572	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169578	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11503907	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12372718	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12427378	0.89[GIH][hapmap];0.93[TSI][hapmap]
rs12818741	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs1316607	0.93[TSI][hapmap]
rs13378012	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs2090852	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs2139930	0.89[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs2280503	0.89[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs34645899	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34863430	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35353300	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742062	0.89[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs4307773	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs4388959	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs4768903	0.82[TSI][hapmap]
rs4986838	0.88[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61926301	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61926303	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7133974	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7137845	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs7297504	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7304335	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7306677	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974517	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs864899	0.92[CEU][hapmap]
rs876080	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs9943712	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1129406	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs1129406	ATF1	cis	Esophagus Muscularis	GTEx
rs1129406	ATF1	cis	Adipose Subcutaneous	GTEx
rs1129406	ATF1	cis	Artery Tibial	GTEx
rs1129406	CERS5	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51180800-51204400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:51188600-51207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:51190200-51204000	Weak transcription	Gastric	stomach
4	chr12:51190200-51215200	Weak transcription	Pancreas	Pancrea
5	chr12:51193200-51204400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:51193200-51207600	Weak transcription	Fetal Heart	heart
7	chr12:51193200-51207800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:51193200-51207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:51193200-51207800	Weak transcription	Esophagus	oesophagus
10	chr12:51193200-51208000	Weak transcription	Small Intestine	intestine
11	chr12:51193200-51211200	Weak transcription	Aorta	Aorta
12	chr12:51193400-51204000	Weak transcription	Psoas Muscle	Psoas
13	chr12:51193400-51207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:51193800-51204200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:51193800-51204400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:51193800-51204400	Weak transcription	Fetal Brain Male	brain
17	chr12:51194000-51203400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:51194000-51203400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:51194000-51204200	Weak transcription	NHLF	lung
20	chr12:51194000-51204400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:51194000-51204400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:51194000-51204400	Weak transcription	NHEK	skin
23	chr12:51194000-51204600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:51194200-51203400	Weak transcription	Brain Substantia Nigra	brain
25	chr12:51194400-51203400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:51194400-51203400	Weak transcription	HUVEC	blood vessel
27	chr12:51194400-51203600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr12:51194400-51204400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:51194400-51204400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:51194400-51204400	Weak transcription	Right Ventricle	heart
31	chr12:51194400-51204400	Weak transcription	HSMMtube	muscle
32	chr12:51194400-51204400	Weak transcription	NH-A	brain
33	chr12:51194400-51204400	Weak transcription	NHDF-Ad	bronchial
34	chr12:51194400-51204600	Weak transcription	Brain Angular Gyrus	brain
35	chr12:51194400-51204600	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:51194400-51207800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:51194600-51203400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:51194600-51204200	Weak transcription	HMEC	breast
39	chr12:51194600-51204400	Weak transcription	Brain Germinal Matrix	brain
40	chr12:51194600-51204400	Weak transcription	Ovary	ovary
41	chr12:51194600-51207800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr12:51194600-51214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:51194800-51203400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:51194800-51204400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:51194800-51209200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:51195000-51203400	Weak transcription	Osteobl	bone
47	chr12:51195200-51203400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:51195600-51203400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:51195600-51203600	Weak transcription	Liver	Liver
50	chr12:51195600-51204000	Weak transcription	Primary hematopoietic stem cells	blood

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