Variant report

Variant	rs7552840
Chromosome Location	chr1:173797226-173797227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:173796630-173797259	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr1:173796616-173797333	SK-N-SH	brain:	n/a	chr1:173797260-173797276

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:173443316..173450639-chr1:173791413..173797919,15	K562	blood:
2	chr1:173397836..173400483-chr1:173795399..173797662,2	K562	blood:
3	chr1:173789792..173811494-chr1:173827886..173840273,103	K562	blood:
4	chr1:173443428..173450639-chr1:173791407..173797248,10	K562	blood:
5	chr1:173797157..173799245-chr1:173831443..173834233,2	MCF-7	breast:
6	chr1:173765402..173769315-chr1:173795358..173797976,3	K562	blood:
7	chr1:173796125..173798114-chr1:173834469..173837018,2	MCF-7	breast:
8	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:
9	chr1:173794468..173797418-chr1:173804249..173806445,2	MCF-7	breast:
10	chr1:173386417..173388679-chr1:173795468..173797775,2	K562	blood:

No data

Variant related genes	Relation type
CENPL	TF binding region
ENSG00000270084	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000208317	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10081990	0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10158663	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10399912	0.86[YRI][hapmap]
rs10798298	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912677	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912678	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912680	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912682	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912684	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1115487	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11487392	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12067571	0.89[AMR][1000 genomes]
rs12070556	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073601	1.00[TSI][hapmap]
rs12080389	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12082206	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12083423	0.88[AMR][1000 genomes]
rs12085748	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12085894	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12094130	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095090	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12096832	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12098124	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1322771	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322772	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375555	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1474907	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846383	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846395	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs16846398	1.00[ASW][hapmap];0.86[YRI][hapmap]
rs16846420	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2224657	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28578576	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4652283	0.90[MKK][hapmap]
rs4652298	0.90[MKK][hapmap]
rs4652328	0.83[MKK][hapmap]
rs56124923	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59845733	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6425256	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs6425257	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6658217	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6663880	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6675762	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6686455	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6689764	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691327	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6692452	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6695782	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6698348	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6702485	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7518130	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7522788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7534521	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536773	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7544583	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7550036	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9282959	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9282960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286886	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286887	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286890	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286894	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425413	0.82[YRI][hapmap]
rs9425414	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs9425415	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9425418	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425419	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425420	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425421	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425422	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425423	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425424	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425426	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425431	0.90[MKK][hapmap]
rs9425433	0.85[MKK][hapmap]
rs9425734	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425736	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425738	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425740	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425741	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425742	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9425746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425747	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425751	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425752	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425758	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425759	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425761	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425768	1.00[ASW][hapmap]
rs9425774	0.83[AMR][1000 genomes]
rs9442660	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9970488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9970633	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7552840	OR9I1	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794200-173804000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:173794400-173802000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:173794400-173806800	Weak transcription	Spleen	Spleen
4	chr1:173794400-173812600	Weak transcription	Small Intestine	intestine
5	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
6	chr1:173794600-173797600	Weak transcription	NHDF-Ad	bronchial
7	chr1:173794600-173799400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:173794600-173799400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:173794600-173799400	Weak transcription	Left Ventricle	heart
10	chr1:173794600-173799600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:173794600-173799600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:173794600-173799800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:173794600-173799800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:173794600-173799800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:173794600-173799800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:173794600-173799800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:173794600-173799800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:173794600-173799800	Weak transcription	Liver	Liver
19	chr1:173794600-173799800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:173794600-173799800	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:173794600-173799800	Weak transcription	Lung	lung
22	chr1:173794600-173799800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:173794600-173800000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:173794600-173803200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:173794600-173804000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:173794600-173805200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:173794600-173805800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:173794600-173805800	Weak transcription	NH-A	brain
29	chr1:173794600-173806000	Weak transcription	HSMMtube	muscle
30	chr1:173794600-173808600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:173794600-173809600	Weak transcription	Fetal Kidney	kidney
32	chr1:173794600-173810600	Weak transcription	Ovary	ovary
33	chr1:173794600-173812400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:173794600-173812600	Weak transcription	Aorta	Aorta
35	chr1:173794600-173813000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:173794600-173814600	Weak transcription	Esophagus	oesophagus
37	chr1:173794600-173820600	Weak transcription	NHLF	lung
38	chr1:173794600-173821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:173794600-173821800	Weak transcription	Pancreas	Pancrea
40	chr1:173794600-173822000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
44	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
45	chr1:173794800-173798800	Weak transcription	Fetal Intestine Small	intestine
46	chr1:173794800-173799400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:173794800-173799400	Weak transcription	Fetal Intestine Large	intestine
48	chr1:173794800-173799800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:173794800-173799800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:173794800-173808200	Weak transcription	Fetal Brain Female	brain

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