Variant report

Variant	rs4413405
Chromosome Location	chr4:7853361-7853362
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	chr4:7804029..7806912-chr4:7851204..7853700,2	MCF-7	breast:
2	chr4:7844578..7847956-chr4:7851101..7853656,4	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10029941	0.85[CHB][hapmap]
rs13109291	0.85[CHB][hapmap]
rs17770936	0.81[CEU][hapmap]
rs2107182	0.85[CHB][hapmap]
rs28393652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28418478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28451112	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28468456	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28508479	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28612887	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28621561	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638094	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28649910	0.86[EUR][1000 genomes]
rs28657375	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28662492	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28728216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861809	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075363	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4234829	0.85[CHB][hapmap]
rs4377592	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383619	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4388087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs4404542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs4473655	1.00[ASW][hapmap];0.91[CEU][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4496581	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4496582	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4552460	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4605652	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4623000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446619	0.85[CHB][hapmap]
rs6828807	0.85[CHB][hapmap]
rs6829473	0.85[CHB][hapmap]
rs6838291	0.91[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6852990	0.85[CHB][hapmap]
rs756255	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4413405	AFAP1	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7821200-7859000	Weak transcription	Aorta	Aorta
2	chr4:7825800-7854200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:7830400-7862600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:7830600-7855200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:7830600-7856200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:7830600-7857200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:7830600-7862200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:7830600-7862400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:7830800-7854400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:7832200-7854000	Weak transcription	Brain Angular Gyrus	brain
11	chr4:7833800-7855200	Weak transcription	Spleen	Spleen
12	chr4:7836600-7855200	Weak transcription	Fetal Kidney	kidney
13	chr4:7840600-7853400	Weak transcription	Pancreas	Pancrea
14	chr4:7843600-7863000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:7845000-7856400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:7845000-7858600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:7845000-7863200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:7845200-7859000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:7846200-7853800	Weak transcription	Stomach Mucosa	stomach
20	chr4:7846200-7860200	Weak transcription	Small Intestine	intestine
21	chr4:7846400-7853400	Weak transcription	Right Atrium	heart
22	chr4:7846400-7857200	Weak transcription	Left Ventricle	heart
23	chr4:7846600-7853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:7846600-7854200	Weak transcription	Brain Substantia Nigra	brain
25	chr4:7846800-7858400	Weak transcription	Fetal Heart	heart
26	chr4:7847000-7854000	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:7847200-7854400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:7847600-7858400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:7847800-7853800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:7847800-7854000	Weak transcription	Esophagus	oesophagus
31	chr4:7847800-7855600	Strong transcription	HSMMtube	muscle
32	chr4:7848000-7854000	Weak transcription	Brain Anterior Caudate	brain
33	chr4:7848000-7857000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:7848000-7857400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:7848000-7857400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr4:7848000-7872200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr4:7848200-7853600	Strong transcription	NH-A	brain
38	chr4:7848200-7854000	Strong transcription	HSMM	muscle
39	chr4:7848200-7854600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr4:7848200-7862000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:7848400-7858200	Weak transcription	Fetal Brain Male	brain
42	chr4:7848600-7856800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:7849200-7854400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:7849200-7857000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:7849400-7857600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:7849600-7853400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:7849600-7854800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:7849800-7854000	Strong transcription	Osteobl	bone
49	chr4:7850000-7854000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:7850000-7857800	Strong transcription	Fetal Intestine Small	intestine

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