Variant report

Variant	rs17123712
Chromosome Location	chr1:63051501-63051502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10493323	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs10493325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1168121	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023489	1.00[JPT][hapmap]
rs12062275	1.00[CHB][hapmap]
rs12563308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563863	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12565895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408480	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17123688	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123721	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];1.00[ASN][1000 genomes]
rs17123725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2016736	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34898550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36157139	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3737890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs55709519	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56094630	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56193814	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56792530	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57022388	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59505425	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59662235	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59816054	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60339595	1.00[EUR][1000 genomes]
rs610248	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs61308091	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61501887	1.00[EUR][1000 genomes]
rs74076653	1.00[EUR][1000 genomes]
rs74076654	1.00[EUR][1000 genomes]
rs74076668	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076670	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076686	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076689	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076691	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076695	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076699	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74076907	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74076909	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74078610	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74078643	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74078661	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9436224	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817371	chr1:62901935-63129697	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1014376	chr1:62976472-63181359	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1011203	chr1:63047046-63081879	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62939800-63060200	Weak transcription	Small Intestine	intestine
2	chr1:62954000-63053400	Weak transcription	Fetal Brain Male	brain
3	chr1:62958200-63061000	Weak transcription	Lung	lung
4	chr1:63000200-63054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:63007200-63056200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:63007200-63096200	Weak transcription	HUVEC	blood vessel
7	chr1:63008400-63053200	Weak transcription	Osteobl	bone
8	chr1:63010800-63078400	Weak transcription	A549	lung
9	chr1:63017800-63057600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:63019800-63052400	Weak transcription	HMEC	breast
11	chr1:63021600-63058800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:63021600-63061400	Weak transcription	Pancreas	Pancrea
13	chr1:63024400-63053200	Weak transcription	NH-A	brain
14	chr1:63026400-63052200	Weak transcription	Primary B cells from cord blood	blood
15	chr1:63026400-63053400	Weak transcription	Primary T cells from cord blood	blood
16	chr1:63028800-63052800	Weak transcription	Esophagus	oesophagus
17	chr1:63035200-63053600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:63036800-63058600	Weak transcription	Fetal Brain Female	brain
19	chr1:63036800-63113600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:63037600-63055000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:63038400-63052200	Weak transcription	GM12878-XiMat	blood
22	chr1:63038400-63054600	Weak transcription	Fetal Kidney	kidney
23	chr1:63038400-63087600	Weak transcription	NHEK	skin
24	chr1:63038400-63095600	Weak transcription	Brain Germinal Matrix	brain
25	chr1:63038600-63052400	Weak transcription	Dnd41	blood
26	chr1:63038600-63083000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:63038800-63053400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:63039000-63063400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:63039200-63095200	Weak transcription	Ovary	ovary
30	chr1:63040400-63052800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:63041000-63095200	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:63041000-63095600	Weak transcription	Fetal Stomach	stomach
33	chr1:63041200-63053800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:63041400-63059000	Weak transcription	Aorta	Aorta
35	chr1:63042200-63083600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:63042400-63056200	Weak transcription	Adipose Nuclei	Adipose
37	chr1:63043400-63056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:63044000-63056000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:63044000-63076000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:63047600-63077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:63048200-63052600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:63048400-63052400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:63048400-63052800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:63050200-63051800	Enhancers	Fetal Intestine Large	intestine
45	chr1:63050200-63052400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:63050200-63052600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr1:63050200-63052600	Strong transcription	HSMM	muscle
48	chr1:63050400-63052000	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr1:63050400-63052400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:63050400-63052800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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