Variant report

Variant	rs1776140
Chromosome Location	chr1:242038713-242038714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:242036963-242038722	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:242036438-242040940	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:242009621..242013856-chr1:242035396..242038763,5	MCF-7	breast:
2	chr1:242011267..242015099-chr1:242035784..242038875,4	K562	blood:
3	chr1:241681618..241683927-chr1:242037772..242040748,2	K562	blood:
4	chr1:242037775..242040488-chr1:242043413..242045224,4	K562	blood:
5	chr1:242030614..242036400-chr1:242037381..242042163,8	K562	blood:
6	chr1:242034800..242036646-chr1:242037118..242039497,2	MCF-7	breast:

No data

Variant related genes	Relation type
EXO1	TF binding region
ENSG00000174371	Chromatin interaction
ENSG00000091483	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1626057	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635510	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1635514	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1635518	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1776130	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776138	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1776141	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1776146	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1776158	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1776159	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1776174	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776176	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1776177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776181	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2298934	0.81[EUR][1000 genomes]
rs2488470	0.83[EUR][1000 genomes]
rs2526698	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526702	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2797600	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797601	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797602	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797603	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2995540	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3121389	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs851778	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs851779	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs851781	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242012200-242044000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:242012400-242060200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:242012600-242051600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:242012600-242051800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:242012800-242054600	Weak transcription	HSMM	muscle
6	chr1:242012800-242056000	Weak transcription	Fetal Intestine Small	intestine
7	chr1:242013000-242053400	Weak transcription	Fetal Lung	lung
8	chr1:242013200-242038800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:242013200-242042000	Weak transcription	HepG2	liver
10	chr1:242013200-242048000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:242013200-242053200	Weak transcription	Osteobl	bone
12	chr1:242013200-242056400	Weak transcription	NHLF	lung
13	chr1:242013400-242049400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:242013400-242055800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:242013600-242039000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:242015600-242038800	Weak transcription	Fetal Intestine Large	intestine
17	chr1:242015800-242041200	Weak transcription	NHEK	skin
18	chr1:242017000-242053800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:242018000-242046600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:242018400-242065600	Weak transcription	Fetal Stomach	stomach
21	chr1:242020800-242038800	Strong transcription	Dnd41	blood
22	chr1:242024600-242043400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:242026400-242082000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:242026800-242052600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:242030000-242038800	Strong transcription	K562	blood
26	chr1:242030400-242063600	Weak transcription	NHDF-Ad	bronchial
27	chr1:242030800-242042200	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:242030800-242053000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:242030800-242054000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:242031000-242042000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:242031000-242046600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:242031000-242047000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:242031000-242054000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:242031000-242054800	Weak transcription	NH-A	brain
35	chr1:242031200-242042200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:242031200-242054200	Weak transcription	HUVEC	blood vessel
37	chr1:242032200-242042200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:242032600-242042200	Weak transcription	GM12878-XiMat	blood
39	chr1:242032600-242045400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:242033800-242042000	Weak transcription	HMEC	breast
41	chr1:242034000-242041200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:242034400-242042000	Weak transcription	A549	lung
43	chr1:242034400-242042000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:242036000-242041000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:242036000-242042200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:242037400-242040200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:242037400-242041400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:242037400-242042000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:242037400-242046600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:242037400-242054400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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