Variant report

Variant	rs1539457
Chromosome Location	chr1:242049849-242049850
allele	C/T
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:27)

rs_ID	r²[population]
rs12564798	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418761	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418762	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539456	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629609	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1632285	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635483	0.84[AFR][1000 genomes]
rs1635484	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635485	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635489	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1635491	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635494	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1635495	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635496	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635499	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1776149	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1776151	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1776152	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1776154	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776156	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149980	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4149984	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150004	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56862550	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851795	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv528015	chr1:241865219-242070731	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv2762521	chr1:241891040-242074222	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv873374	chr1:241975147-242097624	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1008886	chr1:242015591-242176983	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv2750830	chr1:242025098-242303357	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	esv2750831	chr1:242025098-242332959	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv523554	chr1:242029101-242096551	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1002309	chr1:242042242-242295635	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242012400-242060200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:242012600-242051600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:242012600-242051800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:242012800-242054600	Weak transcription	HSMM	muscle
5	chr1:242012800-242056000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:242013000-242053400	Weak transcription	Fetal Lung	lung
7	chr1:242013200-242053200	Weak transcription	Osteobl	bone
8	chr1:242013200-242056400	Weak transcription	NHLF	lung
9	chr1:242013400-242055800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:242017000-242053800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:242018400-242065600	Weak transcription	Fetal Stomach	stomach
12	chr1:242026400-242082000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:242026800-242052600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:242030400-242063600	Weak transcription	NHDF-Ad	bronchial
15	chr1:242030800-242053000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:242030800-242054000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:242031000-242054000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:242031000-242054800	Weak transcription	NH-A	brain
19	chr1:242031200-242054200	Weak transcription	HUVEC	blood vessel
20	chr1:242037400-242054400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:242037600-242054200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:242037600-242065400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:242037800-242050400	Weak transcription	Thymus	Thymus
24	chr1:242040200-242055600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:242040400-242057600	Strong transcription	Dnd41	blood
26	chr1:242040800-242051800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:242041200-242055000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:242041400-242051800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:242042000-242054800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:242042000-242054800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:242042600-242054000	Weak transcription	HMEC	breast
32	chr1:242042600-242056000	Weak transcription	NHEK	skin
33	chr1:242042600-242059600	Weak transcription	HepG2	liver
34	chr1:242042800-242055400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:242043600-242058000	Weak transcription	GM12878-XiMat	blood
36	chr1:242043800-242056200	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:242043800-242065400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:242045000-242050400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:242046800-242063400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:242047000-242056400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:242047200-242054600	Strong transcription	Fetal Thymus	thymus
42	chr1:242047400-242050200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr1:242047400-242053200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:242047800-242051800	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr1:242047800-242051800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:242048000-242050200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:242048000-242050800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:242048000-242051000	Weak transcription	A549	lung
49	chr1:242048000-242051600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr1:242048000-242052600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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