Variant report

Variant	rs1776133
Chromosome Location	chr1:242025098-242025099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:242014950..242016521-chr1:242022226..242025203,2	MCF-7	breast:
2	chr1:242024439..242027110-chr1:242027352..242028876,2	MCF-7	breast:
3	chr1:242022992..242027176-chr1:242044979..242047845,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1627006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1629051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635501	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1635502	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1635507	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1635509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635510	0.92[MKK][hapmap];0.80[YRI][hapmap]
rs1635511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635515	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1776131	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776132	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776134	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1776135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776147	0.82[EUR][1000 genomes]
rs1776178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776180	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236918	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236919	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488471	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2488472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526697	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2526698	0.92[MKK][hapmap];0.80[YRI][hapmap]
rs2526699	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526701	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526704	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2995544	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs735943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851780	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs851782	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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	nsv873373	chr1:241939069-242027500	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1776133	CEP170	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242012000-242032600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:242012200-242025600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:242012200-242027800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:242012200-242028600	Weak transcription	Gastric	stomach
5	chr1:242012200-242044000	Weak transcription	Primary B cells from cord blood	blood
6	chr1:242012400-242060200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:242012600-242051600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:242012600-242051800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:242012800-242054600	Weak transcription	HSMM	muscle
10	chr1:242012800-242056000	Weak transcription	Fetal Intestine Small	intestine
11	chr1:242013000-242053400	Weak transcription	Fetal Lung	lung
12	chr1:242013200-242028800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr1:242013200-242030000	Weak transcription	NHDF-Ad	bronchial
14	chr1:242013200-242030200	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:242013200-242032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:242013200-242034200	Weak transcription	Brain Germinal Matrix	brain
17	chr1:242013200-242036600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:242013200-242038800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:242013200-242042000	Weak transcription	HepG2	liver
20	chr1:242013200-242048000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:242013200-242053200	Weak transcription	Osteobl	bone
22	chr1:242013200-242056400	Weak transcription	NHLF	lung
23	chr1:242013400-242049400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:242013400-242055800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:242013600-242038600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:242013600-242039000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:242014800-242034400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:242015600-242038800	Weak transcription	Fetal Intestine Large	intestine
29	chr1:242015800-242041200	Weak transcription	NHEK	skin
30	chr1:242017000-242053800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:242017400-242026200	Weak transcription	Fetal Brain Female	brain
32	chr1:242017400-242031600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:242017800-242038400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:242018000-242033400	Weak transcription	Placenta	Placenta
35	chr1:242018000-242046600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:242018400-242030200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:242018400-242030200	Weak transcription	Thymus	Thymus
38	chr1:242018400-242065600	Weak transcription	Fetal Stomach	stomach
39	chr1:242019200-242028400	Strong transcription	K562	blood
40	chr1:242019400-242037400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:242019600-242037000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:242019600-242037400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:242020000-242030400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:242020400-242025200	Strong transcription	HUVEC	blood vessel
45	chr1:242020400-242038200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:242020800-242028200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:242020800-242037000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:242020800-242037000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:242020800-242038800	Strong transcription	Dnd41	blood
50	chr1:242021000-242026600	Strong transcription	Hela-S3	cervix

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