Variant report

Variant	rs1572767
Chromosome Location	chr1:184543930-184543931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184542941..184545234-chr1:184556614..184559469,2	K562	blood:
2	chr1:184542941..184545600-chr1:184549233..184551725,2	K562	blood:
3	chr1:184542253..184544072-chr1:184656028..184658362,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10797979	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10911613	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911614	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911618	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12134281	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1339573	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1416752	0.83[MEX][hapmap]
rs1569843	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1569844	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1856562	0.90[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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1969684	0.82[EUR][1000 genomes]
rs1985703	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1999996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4651218	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4651221	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4651224	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs6424958	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6424959	0.89[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6424960	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6667692	0.90[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674023	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674115	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6696816	0.85[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs749214	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]
rs946547	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1572767	C1orf25	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184521000-184547400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:184525000-184546000	Weak transcription	Brain Angular Gyrus	brain
3	chr1:184525600-184544000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:184525600-184545600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:184532400-184545800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:184532600-184545600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:184533200-184547400	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:184536000-184545600	Weak transcription	Left Ventricle	heart
9	chr1:184536000-184559000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:184536000-184559000	Weak transcription	NHEK	skin
11	chr1:184536200-184549200	Weak transcription	NHDF-Ad	bronchial
12	chr1:184536600-184545600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:184536800-184545000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:184536800-184559200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:184537200-184545800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:184537200-184559000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:184538000-184559400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:184538400-184544800	Weak transcription	HSMMtube	muscle
19	chr1:184538400-184558000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:184538400-184558000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:184538400-184559000	Weak transcription	Right Atrium	heart
22	chr1:184538600-184549000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:184538800-184548600	Weak transcription	Fetal Intestine Small	intestine
24	chr1:184539000-184545600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:184543000-184545800	Weak transcription	Fetal Stomach	stomach
26	chr1:184543200-184544200	Enhancers	Psoas Muscle	Psoas
27	chr1:184543200-184544600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:184543400-184544400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr1:184543400-184544600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr1:184543400-184544600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr1:184543400-184544600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:184543400-184544600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:184543600-184544000	Enhancers	Brain Germinal Matrix	brain
34	chr1:184543600-184544000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:184543600-184544200	Enhancers	H9 Cell Line	embryonic stem cell
36	chr1:184543600-184544200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr1:184543600-184544200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:184543600-184544400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr1:184543600-184544400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:184543600-184544400	Enhancers	HSMM	muscle
41	chr1:184543600-184544600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:184543600-184544600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:184543600-184544600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:184543600-184544600	Enhancers	Fetal Lung	lung
45	chr1:184543600-184546200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:184543800-184544000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:184543800-184544000	Enhancers	Esophagus	oesophagus
48	chr1:184543800-184544200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:184543800-184544200	Enhancers	Fetal Muscle Leg	muscle
50	chr1:184543800-184544200	Enhancers	Small Intestine	intestine

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