Variant report

Variant	rs7698368
Chromosome Location	chr4:7933016-7933017
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	chr4:7930429..7933293-chr4:7935968..7937557,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12696835	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1344223	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557817	0.82[CHB][hapmap]
rs2018399	0.82[CHB][hapmap]
rs2385912	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385914	1.00[ASW][hapmap];0.95[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];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28446696	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34072960	0.82[ASN][1000 genomes]
rs4696687	0.93[YRI][hapmap]
rs58349148	0.82[EUR][1000 genomes]
rs6447872	1.00[JPT][hapmap]
rs66479458	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6827395	0.82[CHB][hapmap]
rs6838291	0.82[CHB][hapmap]
rs6840305	0.95[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6846757	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7669433	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7669645	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7695142	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7695170	0.89[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9993085	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7698368	AFAP	cis	multi-tissue	Pritchard
rs7698368	ABLIM2	cis	cerebellum	SCAN
rs7698368	AFAP1	cis	cerebellum	SCAN
rs7698368	WDR1	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
2	chr4:7926600-7936600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:7926800-7935400	Weak transcription	Fetal Brain Male	brain
4	chr4:7930400-7934000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:7930600-7935600	Genic enhancers	Osteobl	bone
6	chr4:7931400-7935400	Weak transcription	Fetal Brain Female	brain
7	chr4:7931400-7939800	Weak transcription	Fetal Kidney	kidney
8	chr4:7931600-7934400	Weak transcription	Fetal Intestine Large	intestine
9	chr4:7931600-7939600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:7931600-7939600	Weak transcription	Ovary	ovary
11	chr4:7931600-7939600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:7931600-7939800	Weak transcription	Lung	lung
13	chr4:7931800-7935400	Weak transcription	Aorta	Aorta
14	chr4:7931800-7935800	Weak transcription	NHDF-Ad	bronchial
15	chr4:7931800-7937200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:7931800-7937600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:7931800-7938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:7931800-7938600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:7931800-7939600	Weak transcription	Brain Angular Gyrus	brain
20	chr4:7932000-7934000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:7932000-7934000	Weak transcription	HSMMtube	muscle
22	chr4:7932000-7934200	Weak transcription	Fetal Stomach	stomach
23	chr4:7932000-7934800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:7932000-7935400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:7932000-7935600	Weak transcription	Gastric	stomach
26	chr4:7932000-7935800	Weak transcription	Stomach Mucosa	stomach
27	chr4:7932000-7936200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:7932000-7937400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:7932000-7938000	Weak transcription	Brain Germinal Matrix	brain
30	chr4:7932000-7938800	Weak transcription	Fetal Lung	lung
31	chr4:7932000-7939600	Weak transcription	Brain Anterior Caudate	brain
32	chr4:7932000-7939600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:7932000-7939600	Weak transcription	Left Ventricle	heart
34	chr4:7932000-7939600	Weak transcription	NHLF	lung
35	chr4:7932000-7939800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:7932000-7939800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:7932000-7939800	Weak transcription	Small Intestine	intestine
38	chr4:7932200-7933200	Enhancers	Hela-S3	cervix
39	chr4:7932200-7934000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr4:7932200-7934800	Weak transcription	Fetal Intestine Small	intestine
41	chr4:7932200-7934800	Weak transcription	NH-A	brain
42	chr4:7932200-7935200	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:7932200-7935400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:7932200-7935400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:7932200-7935400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:7932200-7935400	Weak transcription	HSMM	muscle
47	chr4:7932200-7935800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr4:7932200-7936000	Weak transcription	Colonic Mucosa	Colon
49	chr4:7932200-7936000	Weak transcription	Colon Smooth Muscle	Colon
50	chr4:7932200-7936000	Weak transcription	Right Atrium	heart

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