Variant report

Variant	rs2642182
Chromosome Location	chr1:84630885-84630886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1016379	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027198	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12031206	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031621	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12035258	0.84[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036564	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs12039822	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2139931	1.00[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221360	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2642181	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642183	0.84[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.93[EUR][1000 genomes]
rs2642184	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642185	1.00[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2684911	1.00[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684914	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684916	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2811998	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2811999	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812001	0.98[EUR][1000 genomes]
rs2812447	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2812451	0.84[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812452	0.84[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes]
rs2812453	0.91[EUR][1000 genomes]
rs28810071	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs663521	0.82[ASN][1000 genomes]
rs72710880	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72710887	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72711180	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74095511	0.82[AFR][1000 genomes]
rs7530801	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv546690	chr1:84562265-84655238	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv871731	chr1:84597396-84658591	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv871656	chr1:84601048-84693671	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv997601	chr1:84609346-84672859	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1005225	chr1:84609871-84667950	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1002537	chr1:84611207-84658450	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv999772	chr1:84611207-84667218	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1013911	chr1:84619164-84667950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv871375	chr1:84622793-84678418	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv871643	chr1:84628655-84705481	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84610400-84633400	Weak transcription	Fetal Kidney	kidney
2	chr1:84614000-84633800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:84615800-84634800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:84616200-84635200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:84622400-84635800	Weak transcription	Small Intestine	intestine
6	chr1:84623000-84639200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:84624000-84651800	Weak transcription	Thymus	Thymus
8	chr1:84624800-84633200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:84625600-84635600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:84625800-84634000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:84627200-84631000	Weak transcription	HUVEC	blood vessel
12	chr1:84627600-84635400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:84629200-84636400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:84629200-84654000	Weak transcription	Spleen	Spleen
15	chr1:84629400-84632800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:84629400-84644400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:84629600-84632400	Active TSS	Brain Angular Gyrus	brain
18	chr1:84629600-84632800	Active TSS	Brain Cingulate Gyrus	brain
19	chr1:84629600-84633000	Active TSS	Brain Germinal Matrix	brain
20	chr1:84629600-84633000	Active TSS	Brain Hippocampus Middle	brain
21	chr1:84629600-84633800	Active TSS	Brain Anterior Caudate	brain
22	chr1:84629600-84634000	Active TSS	Fetal Brain Female	brain
23	chr1:84629800-84631400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:84629800-84632000	Active TSS	Brain Substantia Nigra	brain
25	chr1:84629800-84632000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:84629800-84632200	Active TSS	Fetal Brain Male	brain
27	chr1:84629800-84632800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:84629800-84633000	Enhancers	Primary B cells from peripheral blood	blood
29	chr1:84629800-84633200	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:84630000-84631000	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:84630200-84631000	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr1:84630200-84631600	Enhancers	Colon Smooth Muscle	Colon
33	chr1:84630200-84632200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:84630200-84634200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:84630400-84631200	Enhancers	Primary B cells from cord blood	blood
36	chr1:84630400-84633000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:84630600-84631000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:84630600-84631400	Weak transcription	Dnd41	blood
39	chr1:84630600-84632600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:84630600-84633800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:84630600-84635200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr1:84630600-84639800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:84630600-84640400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr1:84630800-84631000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr1:84630800-84631000	Enhancers	NHLF	lung
46	chr1:84630800-84631200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:84630800-84632600	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr1:84630800-84633800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:84630800-84648200	Weak transcription	Primary T cells fromperipheralblood	blood

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