Variant report

Variant	rs749214
Chromosome Location	chr1:184536171-184536172
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	chr1:184356179..184358037-chr1:184532566..184536225,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116667	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10797979	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10911613	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911614	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911618	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12134281	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1339573	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1416752	0.83[MEX][hapmap]
rs1569843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569844	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572767	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1856562	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969684	0.81[EUR][1000 genomes]
rs1985703	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2890014	0.81[AMR][1000 genomes]
rs4651218	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4651221	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4651224	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6424958	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6424959	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6424960	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6667692	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674023	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674115	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696816	0.85[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs946547	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs749214	C1orf25	cis	cerebellum	SCAN
rs749214	CEP350	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184512200-184543600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:184514400-184543800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:184520800-184542000	Weak transcription	Ovary	ovary
4	chr1:184521000-184547400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:184525000-184546000	Weak transcription	Brain Angular Gyrus	brain
6	chr1:184525600-184544000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:184525600-184545600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:184528600-184536400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:184531000-184543800	Weak transcription	Esophagus	oesophagus
10	chr1:184531400-184543200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:184531800-184536600	Weak transcription	Psoas Muscle	Psoas
12	chr1:184531800-184537000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:184531800-184537000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:184531800-184537000	Weak transcription	Right Atrium	heart
15	chr1:184531800-184540600	Weak transcription	Right Ventricle	heart
16	chr1:184531800-184543800	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:184532200-184536400	Weak transcription	Fetal Intestine Small	intestine
18	chr1:184532200-184536600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:184532200-184536600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:184532200-184540600	Weak transcription	Fetal Lung	lung
21	chr1:184532400-184536200	Weak transcription	HSMMtube	muscle
22	chr1:184532400-184536600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:184532400-184536600	Weak transcription	HSMM	muscle
24	chr1:184532400-184545800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:184532600-184536400	Weak transcription	Fetal Heart	heart
26	chr1:184532600-184543600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:184532600-184545600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:184532800-184536200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:184532800-184536600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:184532800-184537800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:184533000-184537800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:184533000-184543800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:184533200-184547400	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:184535200-184536800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:184535200-184536800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:184535200-184536800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:184535200-184537800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:184535200-184538400	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr1:184535200-184538600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:184535400-184536200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:184535400-184536200	Strong transcription	NHDF-Ad	bronchial
42	chr1:184535400-184536600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:184535400-184537200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:184535600-184536200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:184535600-184536600	Weak transcription	Pancreas	Pancrea
46	chr1:184535600-184536600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr1:184535600-184538400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:184535800-184536400	Strong transcription	Lung	lung
49	chr1:184535800-184537200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:184535800-184537200	Enhancers	Placenta Amnion	Placenta Amnion

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