Variant report

Variant	rs1034587
Chromosome Location	chr22:31680240-31680241
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31674730..31677277-chr22:31677970..31680795,3	K562	blood:
2	chr22:31679718..31681431-chr22:31684803..31686641,2	K562	blood:
3	chr22:31675823..31681003-chr22:31682955..31686672,6	MCF-7	breast:
4	chr22:31680141..31683839-chr22:31741911..31744786,3	MCF-7	breast:
5	chr22:31635408..31638175-chr22:31677816..31680372,2	MCF-7	breast:
6	chr22:31675502..31680244-chr22:31686864..31689429,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213888	Chromatin interaction
ENSG00000228839	Chromatin interaction
ENSG00000100100	Chromatin interaction
ENSG00000100105	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1005624	0.85[ASN][1000 genomes]
rs10428007	0.92[ASN][1000 genomes]
rs11089491	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11089495	0.84[ASW][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs1123705	0.82[YRI][hapmap]
rs11556237	0.82[MEX][hapmap]
rs11703005	0.82[MEX][hapmap]
rs11704523	0.82[MEX][hapmap]
rs12627941	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12628752	0.87[ASN][1000 genomes]
rs16989469	0.82[YRI][hapmap]
rs17220369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2027982	0.91[JPT][hapmap]
rs2072193	0.81[JPT][hapmap]
rs2073858	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2074735	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2239905	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2239906	0.94[ASN][1000 genomes]
rs2267169	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2267170	0.86[ASN][1000 genomes]
rs2267171	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2283878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2283880	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2413030	0.85[CEU][hapmap]
rs2413041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28514306	0.80[ASN][1000 genomes]
rs3091392	0.82[MEX][hapmap]
rs34184692	0.87[ASN][1000 genomes]
rs3761431	0.86[CHB][hapmap]
rs3788428	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4561750	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4615	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4618154	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4820952	0.80[ASN][1000 genomes]
rs4820964	0.85[ASN][1000 genomes]
rs4820965	0.90[ASN][1000 genomes]
rs55900008	0.85[ASN][1000 genomes]
rs5749231	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749232	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs5749237	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5749244	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5749246	0.95[EUR][1000 genomes]
rs5749254	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs5753481	0.90[CEU][hapmap]
rs5753482	0.85[CEU][hapmap]
rs5753488	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs5753518	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs5753528	0.92[ASN][1000 genomes]
rs5753531	0.86[ASN][1000 genomes]
rs5753550	0.92[ASN][1000 genomes]
rs5753551	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5753559	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs5753560	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs58315696	0.81[ASN][1000 genomes]
rs5997898	0.91[JPT][hapmap]
rs5997917	0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs5997937	0.84[ASW][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs5997940	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997942	0.84[ASW][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs5997948	0.80[AMR][1000 genomes]
rs61006749	0.87[ASN][1000 genomes]
rs62237404	0.87[ASN][1000 genomes]
rs62237436	0.84[ASN][1000 genomes]
rs68136222	0.92[ASN][1000 genomes]
rs695455	0.82[MEX][hapmap]
rs72617294	0.83[ASN][1000 genomes]
rs72617295	0.87[ASN][1000 genomes]
rs730286	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs73158522	0.83[ASN][1000 genomes]
rs737809	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs738658	0.82[MEX][hapmap]
rs739428	0.82[YRI][hapmap]
rs8143159	0.82[MEX][hapmap]
rs886074	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9609263	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1034587	SLC5A1	cis	parietal	SCAN
rs1034587	DUSP18	cis	parietal	SCAN
rs1034587	BBS1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31654000-31680400	Strong transcription	Lung	lung
2	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
3	chr22:31654200-31680400	Strong transcription	Sigmoid Colon	Sigmoid Colon
4	chr22:31655400-31680800	Weak transcription	K562	blood
5	chr22:31657800-31681200	Strong transcription	Adipose Nuclei	Adipose
6	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
7	chr22:31666000-31682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr22:31666000-31684200	Strong transcription	Aorta	Aorta
9	chr22:31667000-31684600	Weak transcription	Right Atrium	heart
10	chr22:31668400-31681200	Strong transcription	NHLF	lung
11	chr22:31668800-31680400	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr22:31669000-31680400	Strong transcription	Brain Anterior Caudate	brain
13	chr22:31669000-31682200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr22:31669000-31682400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr22:31669000-31685600	Weak transcription	Fetal Brain Male	brain
16	chr22:31669000-31686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr22:31669200-31682600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr22:31669600-31680400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr22:31670000-31680600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr22:31670600-31681000	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr22:31671200-31684600	Weak transcription	Fetal Heart	heart
22	chr22:31671600-31681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr22:31671800-31681000	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr22:31671800-31686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr22:31672000-31680400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr22:31672600-31685600	Strong transcription	Brain Germinal Matrix	brain
27	chr22:31672800-31680600	Strong transcription	Primary B cells from cord blood	blood
28	chr22:31673000-31681800	Strong transcription	Placenta	Placenta
29	chr22:31673800-31685600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr22:31674000-31680400	Strong transcription	Brain Hippocampus Middle	brain
31	chr22:31674000-31680600	Strong transcription	Brain Angular Gyrus	brain
32	chr22:31674000-31681000	Strong transcription	Colonic Mucosa	Colon
33	chr22:31674000-31683800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr22:31674200-31680800	Strong transcription	Right Ventricle	heart
35	chr22:31674200-31682600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr22:31674200-31685400	Strong transcription	Fetal Brain Female	brain
37	chr22:31674400-31680600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr22:31674400-31686400	Weak transcription	Fetal Kidney	kidney
39	chr22:31674400-31686400	Weak transcription	NHDF-Ad	bronchial
40	chr22:31674600-31680400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr22:31674600-31682600	Strong transcription	Rectal Smooth Muscle	rectum
42	chr22:31674800-31680400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr22:31674800-31680400	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr22:31675200-31680400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr22:31675400-31680400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr22:31675400-31681400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr22:31675400-31682200	Strong transcription	Colon Smooth Muscle	Colon
48	chr22:31675400-31686400	Weak transcription	NH-A	brain
49	chr22:31675600-31680800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr22:31675600-31681000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood

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