Variant report

Variant	rs2154138
Chromosome Location	chr1:78330804-78330805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10437022	0.81[CHB][hapmap]
rs10873956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162390	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162400	0.81[CHB][hapmap];0.80[AMR][1000 genomes]
rs1166697	0.80[AMR][1000 genomes]
rs1166701	0.80[AMR][1000 genomes]
rs1166702	0.89[ASW][hapmap];0.81[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1166704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1166705	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1166706	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1166707	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1166709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805735	0.80[AMR][1000 genomes]
rs11807240	0.89[ASW][hapmap];0.81[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12021502	1.00[CEU][hapmap]
rs12405212	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12409561	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1335481	0.81[CHB][hapmap]
rs1536160	0.80[AMR][1000 genomes]
rs1539737	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1555798	0.81[CHB][hapmap];0.80[AMR][1000 genomes]
rs1616949	0.80[AMR][1000 genomes]
rs1626757	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17383213	0.81[CHB][hapmap]
rs17387365	0.81[CHB][hapmap]
rs2274124	1.00[CEU][hapmap]
rs2274257	0.81[CHB][hapmap];0.80[AMR][1000 genomes]
rs2296453	0.81[CHB][hapmap];0.80[AMR][1000 genomes]
rs3767028	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs4949828	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs4949829	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs57421725	0.80[AMR][1000 genomes]
rs6656888	0.89[ASW][hapmap];0.81[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs6659045	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7417104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs750720	0.89[ASW][hapmap];0.81[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs7544892	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9324166	0.80[AMR][1000 genomes]
rs9659938	0.88[ASW][hapmap];0.81[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs9661193	0.80[AMR][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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78282800-78353400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:78284600-78333000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:78285600-78332000	Weak transcription	Spleen	Spleen
4	chr1:78286400-78333200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:78290200-78334200	Weak transcription	Gastric	stomach
6	chr1:78298400-78340400	Weak transcription	Colonic Mucosa	Colon
7	chr1:78298600-78352400	Weak transcription	Right Ventricle	heart
8	chr1:78298800-78332800	Weak transcription	Fetal Kidney	kidney
9	chr1:78299400-78340200	Weak transcription	NHEK	skin
10	chr1:78299400-78341200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:78299600-78340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:78299600-78343000	Weak transcription	K562	blood
13	chr1:78299600-78353800	Weak transcription	Brain Substantia Nigra	brain
14	chr1:78300200-78331600	Weak transcription	Lung	lung
15	chr1:78300200-78332600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:78300800-78342200	Weak transcription	Fetal Brain Male	brain
17	chr1:78301400-78332800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:78301400-78353200	Weak transcription	HSMMtube	muscle
19	chr1:78301800-78342400	Weak transcription	NHLF	lung
20	chr1:78302000-78332000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:78302800-78334200	Weak transcription	HepG2	liver
22	chr1:78303800-78332800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:78305800-78332200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:78305800-78342600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:78306000-78342600	Weak transcription	Brain Angular Gyrus	brain
26	chr1:78309200-78352400	Weak transcription	Aorta	Aorta
27	chr1:78310400-78332000	Weak transcription	Fetal Thymus	thymus
28	chr1:78310600-78331600	Weak transcription	Left Ventricle	heart
29	chr1:78310800-78333000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:78311000-78332600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:78312000-78332800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:78312000-78353000	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:78313000-78331800	Weak transcription	Osteobl	bone
34	chr1:78313000-78353200	Weak transcription	HUVEC	blood vessel
35	chr1:78313400-78343200	Weak transcription	Pancreas	Pancrea
36	chr1:78313800-78332000	Weak transcription	Thymus	Thymus
37	chr1:78316200-78332200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:78320000-78332600	Weak transcription	Brain Anterior Caudate	brain
39	chr1:78321000-78332200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:78321200-78332600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:78323800-78331800	Weak transcription	NHDF-Ad	bronchial
42	chr1:78323800-78340600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:78324400-78334600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:78324400-78334600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:78324600-78331000	Weak transcription	Adipose Nuclei	Adipose
46	chr1:78324600-78353800	Weak transcription	Esophagus	oesophagus
47	chr1:78324800-78332800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:78324800-78334200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:78324800-78340200	Weak transcription	Hela-S3	cervix
50	chr1:78325000-78331000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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