Variant report

Variant	rs6832352
Chromosome Location	chr4:7907592-7907593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7891241..7895444-chr4:7905345..7908483,3	MCF-7	breast:

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10049998	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11932843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13115701	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13131154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137140	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13140004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13145572	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13146302	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13147998	0.93[ASN][1000 genomes]
rs1320073	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435273	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17770147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067842	0.88[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs2385902	0.88[CHB][hapmap]
rs28394221	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492032	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28539821	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28546404	1.00[ASN][1000 genomes]
rs28605531	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613311	0.90[ASN][1000 genomes]
rs28626087	0.85[AMR][1000 genomes]
rs28631977	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28644432	0.81[ASN][1000 genomes]
rs28673208	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28688265	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754920	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2891927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34072304	0.94[ASN][1000 genomes]
rs34075381	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34092549	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34119140	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34121576	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34132874	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34181918	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34189407	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34221000	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34383852	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34392913	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34570748	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34598003	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34652148	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712341	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34868842	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34869495	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34909423	0.94[ASN][1000 genomes]
rs34982807	0.94[ASN][1000 genomes]
rs35114566	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35138920	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35152796	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35154266	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35238070	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35349192	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35502845	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35727635	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35735994	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35881667	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35905776	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35933973	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35967175	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36013696	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36046241	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36106793	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934540	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4234831	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4256209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4296663	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[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4361385	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4411970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4443285	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4447865	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4487321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4579115	0.88[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4689860	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4689865	0.81[JPT][hapmap]
rs4689875	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4696742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696747	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696762	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62289341	0.97[ASN][1000 genomes]
rs62289351	0.97[ASN][1000 genomes]
rs6446624	0.85[ASN][1000 genomes]
rs6446625	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6446627	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.88[ASN][1000 genomes]
rs6446629	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[ASN][1000 genomes]
rs6824266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826598	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6828574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829505	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6837845	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838055	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845014	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855982	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856371	0.81[JPT][hapmap]
rs6856795	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs71600561	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71601887	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71601888	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71601889	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71601890	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71601892	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7660568	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667982	0.81[CHD][hapmap]
rs7682202	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs7682611	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs7683285	0.84[JPT][hapmap]
rs7691386	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694106	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7697255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6832352	AFAP1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7894200-7912400	Weak transcription	Fetal Intestine Large	intestine
2	chr4:7895600-7907600	Weak transcription	Colonic Mucosa	Colon
3	chr4:7896800-7907600	Weak transcription	Fetal Intestine Small	intestine
4	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:7900200-7912400	Weak transcription	NHEK	skin
6	chr4:7900800-7914400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr4:7901000-7909000	Enhancers	Fetal Brain Female	brain
8	chr4:7901400-7909400	Enhancers	Fetal Lung	lung
9	chr4:7901600-7914400	Enhancers	Fetal Muscle Leg	muscle
10	chr4:7902000-7909200	Enhancers	Fetal Heart	heart
11	chr4:7902000-7909400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:7902400-7907600	Enhancers	Rectal Smooth Muscle	rectum
13	chr4:7903400-7911400	Weak transcription	Pancreas	Pancrea
14	chr4:7903400-7911600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:7903600-7915000	Enhancers	Fetal Stomach	stomach
16	chr4:7904200-7909400	Enhancers	Right Atrium	heart
17	chr4:7904400-7909400	Enhancers	NHLF	lung
18	chr4:7904600-7910000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:7904600-7910400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:7904600-7910400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:7904800-7910000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:7904800-7910400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:7904800-7911200	Weak transcription	Gastric	stomach
24	chr4:7904800-7912200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:7905000-7911200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:7905200-7907800	Weak transcription	Stomach Mucosa	stomach
27	chr4:7905200-7911200	Weak transcription	Small Intestine	intestine
28	chr4:7905200-7911800	Weak transcription	Aorta	Aorta
29	chr4:7905400-7908200	Enhancers	Brain Anterior Caudate	brain
30	chr4:7905400-7908600	Flanking Active TSS	Osteobl	bone
31	chr4:7905600-7907800	Enhancers	Colon Smooth Muscle	Colon
32	chr4:7905600-7908000	Flanking Active TSS	NHDF-Ad	bronchial
33	chr4:7905600-7908400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:7905600-7908400	Enhancers	Brain Angular Gyrus	brain
35	chr4:7905600-7909200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr4:7905600-7912400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:7905800-7908000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:7905800-7908600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:7905800-7908600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:7905800-7909000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:7905800-7909200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:7905800-7909200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr4:7905800-7909200	Enhancers	Fetal Kidney	kidney
44	chr4:7905800-7909400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:7905800-7909400	Enhancers	Fetal Thymus	thymus
46	chr4:7906000-7907800	Enhancers	Brain Substantia Nigra	brain
47	chr4:7906000-7908800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr4:7906000-7909000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr4:7906000-7909200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:7906000-7909400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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