Variant report

Variant	rs12122759
Chromosome Location	chr1:227217340-227217341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227203735..227207189-chr1:227216806..227218910,3	K562	blood:
2	chr1:227216840..227218433-chr1:227220852..227222970,2	K562	blood:
3	chr1:227216665..227219394-chr1:227921032..227923176,2	K562	blood:

Variant related genes	Relation type
ENSG00000081692	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1045247	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10495259	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10495271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10495272	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916079	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11583340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11586575	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11586734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12117207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12118022	0.83[EUR][1000 genomes]
rs12121729	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12127665	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12128667	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12131913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12133428	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12134379	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12136857	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12141838	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12739480	0.81[CEU][hapmap]
rs12744825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12751015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12752546	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12755437	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1320495	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17544956	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17545704	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17592190	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17601316	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17601919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17602169	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2150874	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34169114	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34556998	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34653494	0.82[EUR][1000 genomes]
rs35156994	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35651721	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35817866	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738727	0.84[EUR][1000 genomes]
rs3768422	0.85[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3768431	0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3820651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308948	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs61836468	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664330	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6674640	1.00[YRI][hapmap]
rs6681959	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6695431	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698156	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7512871	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs7526822	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[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7538237	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1007352	chr1:227196502-227247160	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv997751	chr1:227196502-227263537	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1010864	chr1:227199493-227246753	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014423	chr1:227201253-227268843	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1012482	chr1:227212024-227271750	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12122759	ITPKB	cis	parietal	SCAN
rs12122759	CABC1	cis	parietal	SCAN
rs12122759	SNAP47	cis	parietal	SCAN
rs12122759	CDC42BPA	cis	lymphoblastoid	seeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
3	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
4	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
6	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
8	chr1:227184000-227234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:227187200-227218600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:227190600-227223200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:227190600-227272600	Weak transcription	Lung	lung
12	chr1:227192600-227220200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:227192800-227220200	Weak transcription	Gastric	stomach
14	chr1:227202600-227222600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
16	chr1:227205600-227220400	Weak transcription	Stomach Mucosa	stomach
17	chr1:227207600-227242000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:227208800-227222600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:227209000-227231000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:227209000-227234600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:227209000-227272400	Weak transcription	Fetal Intestine Small	intestine
22	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:227209800-227222800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:227210200-227226400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:227210600-227245800	Weak transcription	NHEK	skin
26	chr1:227212200-227223000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:227212600-227217600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:227212800-227226400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:227213000-227219200	Strong transcription	Liver	Liver
30	chr1:227213200-227222400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:227213400-227217400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:227213400-227220000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:227213600-227217400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:227213600-227217400	Strong transcription	K562	blood
35	chr1:227213600-227228000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:227213800-227217600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:227213800-227222000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr1:227214000-227220800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:227214000-227222600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:227214200-227217600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:227214200-227220200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:227214400-227217400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:227214400-227218000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:227214600-227221600	Weak transcription	Fetal Heart	heart
45	chr1:227214600-227226200	Weak transcription	Brain Germinal Matrix	brain
46	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
47	chr1:227215000-227222400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:227215200-227217600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:227215200-227220000	Weak transcription	Aorta	Aorta
50	chr1:227215400-227219000	Strong transcription	HMEC	breast

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