Variant report

Variant	rs4953843
Chromosome Location	chr2:110366503-110366504
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	chr2:110365749..110368166-chr2:110372173..110374120,2	MCF-7	breast:
2	chr2:110363990..110367269-chr2:110379500..110381525,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10175432	0.84[ASN][1000 genomes]
rs11541143	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[ASN][1000 genomes]
rs12998808	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1434167	0.81[EUR][1000 genomes]
rs2018352	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2043462	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060402	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060403	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28369323	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs28544318	0.94[ASN][1000 genomes]
rs28567471	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28583991	0.92[ASN][1000 genomes]
rs28588372	0.82[ASN][1000 genomes]
rs28615410	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28624186	0.81[ASN][1000 genomes]
rs2867277	0.80[ASN][1000 genomes]
rs28728215	0.90[ASN][1000 genomes]
rs34557890	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3923006	0.89[ASN][1000 genomes]
rs3934873	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4953760	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953784	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4953850	0.90[ASN][1000 genomes]
rs56288075	0.80[EUR][1000 genomes]
rs56364682	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56402128	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61548546	0.82[ASN][1000 genomes]
rs6594037	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6594041	0.81[ASN][1000 genomes]
rs6594049	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6705503	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs6723295	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6726252	0.90[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6745809	0.94[ASN][1000 genomes]
rs6748632	0.89[ASN][1000 genomes]
rs6760478	0.82[ASN][1000 genomes]
rs747445	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7596172	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs767628	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs892460	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892464	0.82[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs919941	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330311	0.82[ASN][1000 genomes]
rs9330320	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9330324	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription 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 miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv829617	chr2:110359857-110380012	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4953843	SEPT10	cis	parietal	SCAN
rs4953843	ACOXL	cis	cerebellum	SCAN
rs4953843	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
2	chr2:110324000-110370400	Weak transcription	Esophagus	oesophagus
3	chr2:110329000-110369000	Weak transcription	Ovary	ovary
4	chr2:110329200-110369400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:110350200-110367000	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:110350400-110369200	Weak transcription	Fetal Stomach	stomach
7	chr2:110352600-110369200	Weak transcription	Fetal Brain Female	brain
8	chr2:110352800-110369400	Weak transcription	Brain Germinal Matrix	brain
9	chr2:110358800-110367000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:110358800-110370200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:110359400-110366600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:110359600-110369400	Weak transcription	Fetal Kidney	kidney
13	chr2:110359800-110369200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:110359800-110370200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:110359800-110370600	Weak transcription	Brain Angular Gyrus	brain
16	chr2:110360000-110367000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:110360800-110369200	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:110362000-110366800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:110362200-110366600	Enhancers	Hela-S3	cervix
20	chr2:110362200-110366800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:110362200-110367000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr2:110362400-110369200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:110362400-110370200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:110362600-110366800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:110362600-110366800	Weak transcription	Adipose Nuclei	Adipose
26	chr2:110362600-110369000	Weak transcription	Psoas Muscle	Psoas
27	chr2:110362600-110370400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:110362800-110366600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:110362800-110367000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:110363200-110367600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:110363400-110366800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:110363400-110366800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:110363400-110367200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:110363600-110366600	Enhancers	HUVEC	blood vessel
35	chr2:110363600-110367000	Enhancers	NHDF-Ad	bronchial
36	chr2:110363800-110367000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:110363800-110367200	Weak transcription	Fetal Lung	lung
38	chr2:110363800-110369000	Weak transcription	Placenta	Placenta
39	chr2:110363800-110369200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:110363800-110369800	Weak transcription	Right Ventricle	heart
41	chr2:110364000-110366600	Enhancers	Osteobl	bone
42	chr2:110364000-110369200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:110364200-110366600	Enhancers	NHLF	lung
44	chr2:110364400-110366800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:110364400-110368000	Enhancers	Fetal Intestine Small	intestine
46	chr2:110364600-110366800	Weak transcription	Fetal Heart	heart
47	chr2:110364600-110367000	Weak transcription	Left Ventricle	heart
48	chr2:110364600-110367000	Weak transcription	Right Atrium	heart
49	chr2:110364600-110367600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:110364600-110367600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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