Variant report

Variant	rs4758649
Chromosome Location	chr12:122749234-122749235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122708152..122712753-chr12:122748620..122752557,8	K562	blood:
2	chr12:122740776..122742796-chr12:122748119..122749957,2	MCF-7	breast:
3	chr12:122748134..122753515-chr12:122760156..122766963,8	K562	blood:
4	chr12:122743004..122745567-chr12:122747248..122750605,3	MCF-7	breast:
5	chr12:122740036..122743044-chr12:122748380..122750717,3	MCF-7	breast:
6	chr12:122747009..122749656-chr12:122904733..122907639,2	K562	blood:
7	chr12:122707649..122712350-chr12:122748538..122752681,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184047	Chromatin interaction
ENSG00000130779	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10270	0.83[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10848035	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11060167	0.95[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11060333	0.95[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs12423987	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12424872	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12425684	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12578739	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12578815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12578863	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12578953	0.89[ASN][1000 genomes]
rs12580084	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs12809220	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12810587	0.91[CEU][hapmap]
rs12811503	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12814516	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12814554	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12814923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12815053	0.82[EUR][1000 genomes]
rs12816400	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12816499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12820704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12822121	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12824385	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12824701	0.91[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.83[EUR][1000 genomes]
rs12824925	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12825008	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12825149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12825279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12826834	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12827843	0.83[EUR][1000 genomes]
rs12831210	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1512023	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1967291	0.91[EUR][1000 genomes]
rs2063510	0.86[JPT][hapmap]
rs2068223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271408	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2271409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277332	0.86[JPT][hapmap]
rs2277333	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34325222	0.83[ASN][1000 genomes]
rs34383196	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35030971	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35772530	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35963777	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782153	0.85[EUR][1000 genomes]
rs3782154	0.86[JPT][hapmap]
rs3809116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4567503	0.86[JPT][hapmap]
rs4758650	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs4758670	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs4758677	0.95[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6488906	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488909	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7313284	1.00[YRI][hapmap]
rs7388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962385	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs7963565	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs7964911	0.81[ASN][1000 genomes]
rs7970027	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs872451	0.91[CEU][hapmap]
rs907482	0.83[CEU][hapmap];0.86[JPT][hapmap]

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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4758649	GPR109A	cis	cerebellum	SCAN
rs4758649	VPS33A	cis	multi-tissue	Pritchard
rs4758649	MLXIP	Cis_1M	lymphoblastoid	RTeQTL
rs4758649	ENSG00000139719	cis	multi-tissue	Pritchard
rs4758649	IL31	cis	parietal	SCAN
rs4758649	VPS33A	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122711800-122749600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:122711800-122749600	Weak transcription	Psoas Muscle	Psoas
3	chr12:122716000-122749600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:122716000-122750200	Weak transcription	Fetal Kidney	kidney
5	chr12:122717200-122750000	Weak transcription	Fetal Heart	heart
6	chr12:122720600-122750000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:122720600-122750200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:122721600-122750400	Weak transcription	Small Intestine	intestine
9	chr12:122722000-122750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:122730600-122749600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr12:122733400-122749600	Weak transcription	Colonic Mucosa	Colon
12	chr12:122733400-122750000	Weak transcription	HSMMtube	muscle
13	chr12:122733600-122749600	Weak transcription	HMEC	breast
14	chr12:122734200-122749600	Weak transcription	HepG2	liver
15	chr12:122735400-122749600	Weak transcription	Stomach Mucosa	stomach
16	chr12:122735400-122750000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:122737600-122749600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:122741200-122749400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:122741600-122750000	Weak transcription	Brain Substantia Nigra	brain
20	chr12:122741800-122749600	Weak transcription	Pancreas	Pancrea
21	chr12:122742600-122749600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:122742800-122749800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:122743200-122749400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:122743400-122749800	Weak transcription	Brain Angular Gyrus	brain
25	chr12:122743800-122749800	Weak transcription	K562	blood
26	chr12:122745400-122749800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:122746000-122749600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:122746000-122749600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:122746000-122749800	Weak transcription	HUVEC	blood vessel
30	chr12:122746000-122750200	Weak transcription	Esophagus	oesophagus
31	chr12:122746200-122749400	Weak transcription	GM12878-XiMat	blood
32	chr12:122746200-122749600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:122746200-122749600	Weak transcription	NHEK	skin
34	chr12:122746200-122750000	Weak transcription	HSMM	muscle
35	chr12:122746200-122750000	Weak transcription	NH-A	brain
36	chr12:122746200-122750000	Weak transcription	NHDF-Ad	bronchial
37	chr12:122746200-122750200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:122746200-122750200	Weak transcription	Gastric	stomach
39	chr12:122746200-122750400	Weak transcription	Aorta	Aorta
40	chr12:122746400-122749600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:122746400-122749600	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:122746400-122749600	Weak transcription	Fetal Brain Female	brain
43	chr12:122746400-122750400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:122746400-122750400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:122746800-122749600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:122746800-122750000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:122747000-122749600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:122747000-122749600	Weak transcription	Brain Germinal Matrix	brain
49	chr12:122747000-122749800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:122747000-122750200	Weak transcription	Colon Smooth Muscle	Colon

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