Variant report

Variant	rs2277332
Chromosome Location	chr12:122750700-122750701
allele	A/C
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122708152..122712753-chr12:122748620..122752557,8	K562	blood:
2	chr12:122459684..122462243-chr12:122749527..122751932,2	MCF-7	breast:
3	chr12:122748134..122753515-chr12:122760156..122766963,8	K562	blood:
4	chr12:122688160..122690771-chr12:122750336..122752523,2	MCF-7	breast:
5	chr12:122740036..122743044-chr12:122748380..122750717,3	MCF-7	breast:
6	chr12:122750460..122753402-chr12:122760156..122762778,3	K562	blood:
7	chr12:122709035..122711225-chr12:122749359..122751433,5	MCF-7	breast:
8	chr1:228635449..228637961-chr12:122750153..122751748,2	MCF-7	breast:
9	chr12:122707649..122712350-chr12:122748538..122752681,8	K562	blood:
10	chr12:122749733..122752495-chr12:122984163..122985921,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000230841	Chromatin interaction
ENSG00000184047	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000130779	Chromatin interaction
ENSG00000176383	Chromatin interaction
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10270	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10846470	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11061609	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12423987	0.86[JPT][hapmap]
rs12424872	0.96[CEU][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs12578815	0.80[JPT][hapmap]
rs12578953	0.88[EUR][1000 genomes]
rs12580084	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12809220	0.84[ASN][1000 genomes]
rs12810587	0.87[CEU][hapmap]
rs12814923	0.85[JPT][hapmap]
rs12815512	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12816499	0.84[JPT][hapmap]
rs12820704	0.81[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs12822121	0.85[JPT][hapmap]
rs12824701	1.00[JPT][hapmap]
rs12824925	0.90[JPT][hapmap]
rs12825149	0.90[JPT][hapmap]
rs12825279	0.86[JPT][hapmap]
rs12828234	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12833379	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1512023	0.90[JPT][hapmap]
rs2063510	0.87[ASW][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs2068223	0.80[JPT][hapmap]
rs2271409	0.86[JPT][hapmap]
rs34325222	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782153	0.88[ASN][1000 genomes]
rs3782154	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809116	0.80[JPT][hapmap]
rs4567503	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4758649	0.86[JPT][hapmap]
rs4758650	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758670	0.82[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758671	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55741463	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59734396	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6488876	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298397	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7388	0.86[JPT][hapmap]
rs7957569	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962385	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963144	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7963565	0.96[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7964911	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7965868	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7970027	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972228	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs872451	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs907482	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907483	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9668064	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2277332	GPR109A	cis	cerebellum	SCAN
rs2277332	IL31	cis	parietal	SCAN
rs2277332	VPS33A	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122749400-122752000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr12:122749600-122751000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:122749600-122751800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr12:122749600-122751800	Active TSS	Thymus	Thymus
5	chr12:122749600-122752000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:122749800-122750800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:122749800-122750800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr12:122749800-122751800	Active TSS	K562	blood
9	chr12:122749800-122752000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:122749800-122752000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:122749800-122752000	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:122749800-122752000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:122749800-122752200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:122750000-122750800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr12:122750000-122750800	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr12:122750000-122750800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr12:122750000-122751000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr12:122750000-122751800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:122750000-122751800	Active TSS	Fetal Brain Male	brain
20	chr12:122750000-122751800	Active TSS	Fetal Intestine Large	intestine
21	chr12:122750000-122751800	Active TSS	Fetal Intestine Small	intestine
22	chr12:122750000-122751800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:122750000-122751800	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr12:122750000-122751800	Active TSS	A549	lung
25	chr12:122750000-122751800	Active TSS	HSMM	muscle
26	chr12:122750000-122751800	Active TSS	HSMMtube	muscle
27	chr12:122750000-122752000	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr12:122750000-122752000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:122750000-122752000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:122750000-122752000	Active TSS	Right Atrium	heart
31	chr12:122750000-122752200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:122750200-122750800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr12:122750200-122750800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr12:122750200-122750800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr12:122750200-122750800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:122750200-122750800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:122750200-122750800	Flanking Active TSS	Placenta	Placenta
38	chr12:122750200-122751000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr12:122750200-122751400	Active TSS	Fetal Muscle Trunk	muscle
40	chr12:122750200-122751400	Bivalent/Poised TSS	HepG2	liver
41	chr12:122750200-122751600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr12:122750200-122751600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:122750200-122751600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:122750200-122751600	Active TSS	Gastric	stomach
45	chr12:122750200-122751800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:122750200-122751800	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr12:122750200-122751800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:122750200-122751800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:122750200-122751800	Active TSS	Brain Anterior Caudate	brain
50	chr12:122750200-122751800	Active TSS	Esophagus	oesophagus

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