Variant report

Variant	rs7554793
Chromosome Location	chr1:171680912-171680913
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10489250	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10913484	0.84[EUR][1000 genomes]
rs12021915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12022661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12024194	0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs12024335	0.82[ASN][1000 genomes]
rs12028096	0.83[ASN][1000 genomes]
rs12034114	0.85[ASN][1000 genomes]
rs12036980	0.89[CHB][hapmap]
rs12089083	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12095503	0.82[EUR][1000 genomes]
rs12566700	0.81[CEU][hapmap]
rs16843227	0.97[ASN][1000 genomes]
rs2421910	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs57300412	0.97[ASN][1000 genomes]
rs58081399	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61413126	0.96[ASN][1000 genomes]
rs6659266	0.98[ASN][1000 genomes]
rs6665590	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665614	0.94[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs6670549	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6695031	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72717895	0.85[ASN][1000 genomes]
rs72717900	0.98[ASN][1000 genomes]
rs72719512	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1800458	chr1:171667663-171701129	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171664400-171685800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:171664800-171684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
4	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:171666000-171685000	Weak transcription	Brain Germinal Matrix	brain
7	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
8	chr1:171666200-171682600	Weak transcription	Lung	lung
9	chr1:171666200-171684600	Weak transcription	Fetal Stomach	stomach
10	chr1:171666200-171684800	Weak transcription	Thymus	Thymus
11	chr1:171666600-171684800	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:171666600-171686200	Weak transcription	Gastric	stomach
13	chr1:171666800-171686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:171667000-171685000	Weak transcription	Osteobl	bone
19	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
20	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
21	chr1:171667600-171681200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:171667600-171692000	Weak transcription	Fetal Lung	lung
23	chr1:171667800-171688400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:171667800-171688800	Weak transcription	Spleen	Spleen
25	chr1:171667800-171692000	Weak transcription	Fetal Thymus	thymus
26	chr1:171668000-171685800	Weak transcription	Esophagus	oesophagus
27	chr1:171668600-171684800	Weak transcription	Fetal Kidney	kidney
28	chr1:171668600-171692400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:171668800-171705400	Weak transcription	Right Ventricle	heart
30	chr1:171668800-171708200	Weak transcription	Small Intestine	intestine
31	chr1:171669400-171685800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:171669600-171685800	Weak transcription	NHEK	skin
33	chr1:171669600-171705400	Weak transcription	Fetal Brain Male	brain
34	chr1:171670000-171688200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:171670600-171685600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:171670600-171692000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:171671200-171685000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:171672800-171685800	Weak transcription	K562	blood
39	chr1:171672800-171686200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:171672800-171692000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:171673600-171686800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:171674000-171696400	Weak transcription	HSMM	muscle
43	chr1:171674200-171686000	Weak transcription	Stomach Mucosa	stomach
44	chr1:171674600-171684800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:171674600-171686000	Weak transcription	HSMMtube	muscle
46	chr1:171674600-171692200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:171674800-171696800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:171674800-171697200	Weak transcription	Ovary	ovary
49	chr1:171675000-171684400	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:171675000-171684400	Weak transcription	Stomach Smooth Muscle	stomach

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