Variant report

Variant	rs12667132
Chromosome Location	chr7:129020020-129020021
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:129018273..129020957-chr7:129031005..129033458,2	K562	blood:
2	chr7:129014837..129017085-chr7:129019916..129023036,4	K562	blood:

Variant related genes	Relation type
ENSG00000158467	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1000676	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10248810	0.86[JPT][hapmap]
rs10954226	0.86[JPT][hapmap]
rs10954228	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10954229	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10954230	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10954231	0.83[ASN][1000 genomes]
rs11979476	0.86[JPT][hapmap]
rs12112374	0.86[JPT][hapmap]
rs12534372	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12540568	0.80[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12667232	0.82[TSI][hapmap]
rs12668958	0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs12671604	0.82[TSI][hapmap]
rs1526900	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs1541711	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1559486	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs17168734	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17168750	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1880854	0.86[JPT][hapmap]
rs2694572	0.86[JPT][hapmap]
rs2694574	0.84[JPT][hapmap]
rs2718083	0.80[JPT][hapmap]
rs2718084	0.81[JPT][hapmap]
rs34022136	0.98[ASN][1000 genomes]
rs35305688	0.85[ASN][1000 genomes]
rs35366945	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35974655	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4460315	0.83[ASN][1000 genomes]
rs4728162	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4728163	0.84[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4728164	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4731572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4731573	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4731575	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6467233	0.81[JPT][hapmap]
rs6966595	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs6980385	0.86[JPT][hapmap]
rs753336	0.82[TSI][hapmap]
rs7788327	0.86[JPT][hapmap]
rs822038	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs822040	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs891545	0.81[JPT][hapmap]
rs963465	0.81[JPT][hapmap]
rs9641846	0.81[JPT][hapmap]
rs9641850	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9641851	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs966481	0.82[TSI][hapmap]
rs974558	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12667132	AHCYL2	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128989200-129044200	Weak transcription	Ovary	ovary
2	chr7:129006200-129046000	Weak transcription	Aorta	Aorta
3	chr7:129008200-129035000	Weak transcription	Psoas Muscle	Psoas
4	chr7:129008400-129044200	Weak transcription	Fetal Muscle Leg	muscle
5	chr7:129008400-129073200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:129008600-129037200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:129008800-129023400	Weak transcription	Primary B cells from cord blood	blood
8	chr7:129008800-129025200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:129008800-129035000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr7:129008800-129035000	Weak transcription	Fetal Stomach	stomach
11	chr7:129008800-129035200	Weak transcription	Lung	lung
12	chr7:129008800-129039800	Weak transcription	Placenta	Placenta
13	chr7:129009000-129020600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr7:129009000-129028400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr7:129010400-129041000	Weak transcription	Esophagus	oesophagus
16	chr7:129011400-129030400	Weak transcription	Fetal Intestine Small	intestine
17	chr7:129015200-129029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:129015600-129027600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:129015600-129028200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:129015800-129027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:129015800-129028200	Weak transcription	Brain Substantia Nigra	brain
22	chr7:129015800-129029200	Weak transcription	Fetal Brain Female	brain
23	chr7:129015800-129053400	Weak transcription	Fetal Lung	lung
24	chr7:129016000-129022200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:129016000-129024600	Weak transcription	Brain Anterior Caudate	brain
26	chr7:129016000-129027600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:129016000-129028200	Weak transcription	Brain Germinal Matrix	brain
28	chr7:129016000-129029400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:129016000-129062400	Weak transcription	Pancreas	Pancrea
30	chr7:129016000-129071400	Weak transcription	Small Intestine	intestine
31	chr7:129016400-129024600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:129016400-129025000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:129016400-129052400	Weak transcription	Fetal Kidney	kidney
34	chr7:129016600-129024400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:129016600-129028800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr7:129016600-129035000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr7:129016600-129055200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:129017000-129027800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr7:129017200-129026400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:129017400-129024400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr7:129017400-129027600	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:129017400-129029000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:129017400-129030000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:129017400-129030400	Weak transcription	Colonic Mucosa	Colon
45	chr7:129017400-129035000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr7:129017400-129041000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr7:129017400-129051800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:129017400-129069200	Weak transcription	Stomach Mucosa	stomach
49	chr7:129017400-129073000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr7:129017600-129021600	Weak transcription	GM12878-XiMat	blood

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