Variant report

Variant	rs735943
Chromosome Location	chr1:242030151-242030152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:242026543..242030439-chr1:242041190..242044966,5	K562	blood:
2	chr1:242026426..242029268-chr1:242029901..242034404,4	K562	blood:

Variant related genes	Relation type
ENSG00000174371	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1627006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1629051	0.99[AMR][1000 genomes];0.98[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];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1635502	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1635507	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1635509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635510	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1635511	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635512	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635515	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[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];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1776130	0.82[AFR][1000 genomes]
rs1776131	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776132	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776133	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776134	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1776135	0.99[AMR][1000 genomes];0.99[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];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776147	0.83[EUR][1000 genomes]
rs1776174	0.94[AFR][1000 genomes]
rs1776178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776180	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1776181	0.84[YRI][hapmap]
rs2236918	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236919	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298934	0.85[AFR][1000 genomes]
rs2488471	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2488472	0.99[AMR][1000 genomes];0.99[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];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2526698	0.84[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2526699	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526701	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526704	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797601	0.94[AFR][1000 genomes]
rs2797602	0.86[AFR][1000 genomes]
rs2995544	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs851780	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs851781	0.87[LWK][hapmap]
rs851782	0.89[AMR][1000 genomes];0.99[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs735943	CEP170	cis	cerebellum	SCAN

Chromatin state (count:69 , 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	chr1:242012200-242044000	Weak transcription	Primary B cells from cord blood	blood
3	chr1:242012400-242060200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:242012600-242051600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:242012600-242051800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:242012800-242054600	Weak transcription	HSMM	muscle
7	chr1:242012800-242056000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:242013000-242053400	Weak transcription	Fetal Lung	lung
9	chr1:242013200-242030200	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:242013200-242032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:242013200-242034200	Weak transcription	Brain Germinal Matrix	brain
12	chr1:242013200-242036600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:242013200-242038800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:242013200-242042000	Weak transcription	HepG2	liver
15	chr1:242013200-242048000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:242013200-242053200	Weak transcription	Osteobl	bone
17	chr1:242013200-242056400	Weak transcription	NHLF	lung
18	chr1:242013400-242049400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:242013400-242055800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:242013600-242038600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:242013600-242039000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:242014800-242034400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:242015600-242038800	Weak transcription	Fetal Intestine Large	intestine
24	chr1:242015800-242041200	Weak transcription	NHEK	skin
25	chr1:242017000-242053800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:242017400-242031600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:242017800-242038400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:242018000-242033400	Weak transcription	Placenta	Placenta
29	chr1:242018000-242046600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:242018400-242030200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:242018400-242030200	Weak transcription	Thymus	Thymus
32	chr1:242018400-242065600	Weak transcription	Fetal Stomach	stomach
33	chr1:242019400-242037400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:242019600-242037000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:242019600-242037400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:242020000-242030400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:242020400-242038200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:242020800-242037000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:242020800-242037000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:242020800-242038800	Strong transcription	Dnd41	blood
41	chr1:242021600-242032600	Strong transcription	GM12878-XiMat	blood
42	chr1:242023000-242034800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:242024000-242032400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:242024600-242035400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:242024600-242043400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:242024800-242030200	Weak transcription	NH-A	brain
47	chr1:242025200-242030200	Weak transcription	HMEC	breast
48	chr1:242025200-242030200	Weak transcription	HUVEC	blood vessel
49	chr1:242025200-242035600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:242025800-242030200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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