Variant report

Variant	rs4690001
Chromosome Location	chr4:2875140-2875141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:2874928-2875433	T-47D	breast:	n/a	chr4:2875285-2875292
2	FOXA1	chr4:2875099-2875341	T-47D	breast:	n/a	n/a
3	FOXA1	chr4:2875059-2875359	T-47D	breast:	n/a	n/a
4	GATA3	chr4:2874947-2875464	T-47D	breast:	n/a	chr4:2875285-2875292
5	JUND	chr4:2875009-2875513	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2873606..2876373-chr4:2925507..2927684,2	MCF-7	breast:
2	chr4:2873287..2875371-chr4:2875676..2877933,2	K562	blood:
3	chr4:2846265..2848875-chr4:2873594..2875378,2	K562	blood:
4	chr4:2867163..2870465-chr4:2873616..2875440,4	K562	blood:

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1012365	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs1242228	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1263338	0.80[ASN][1000 genomes]
rs1263339	0.85[ASN][1000 genomes]
rs1263342	0.84[ASN][1000 genomes]
rs1263344	0.84[ASN][1000 genomes]
rs1263345	0.91[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1263347	0.91[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1263349	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.81[YRI][hapmap]
rs1263359	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1263360	0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs12642795	0.88[ASN][1000 genomes]
rs12645803	0.81[AMR][1000 genomes]
rs1419045	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs16843452	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16843523	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2051560	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs2071695	0.83[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs2097081	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2185885	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2237004	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs2239728	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs2282772	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2282773	0.87[ASN][1000 genomes]
rs2282774	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2285084	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs3775068	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs3796469	0.94[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4690000	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4690065	0.86[ASN][1000 genomes]
rs4961	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs4963	0.83[CEU][hapmap];0.83[ASN][1000 genomes]
rs4964	0.83[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs73082333	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73189448	0.87[EUR][1000 genomes]
rs73189458	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs762847	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs7654786	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7664801	0.80[AMR][1000 genomes];0.87[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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
3	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4690001	DGKQ	cis	parietal	SCAN
rs4690001	ZNF732	cis	cerebellum	SCAN
rs4690001	ZFYVE28	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2857000-2877000	Weak transcription	Dnd41	blood
2	chr4:2857400-2877600	Weak transcription	HMEC	breast
3	chr4:2864600-2877400	Weak transcription	NHEK	skin
4	chr4:2870000-2877400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:2870000-2877600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:2870200-2877000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:2870600-2886000	Weak transcription	Fetal Brain Male	brain
9	chr4:2870800-2877800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:2870800-2878800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:2871000-2875800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:2871000-2877600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:2871000-2885800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:2871200-2875400	Weak transcription	NHLF	lung
15	chr4:2871200-2877000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:2871200-2877000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:2871200-2877400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:2871200-2877400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:2871200-2877400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:2871200-2877400	Weak transcription	Placenta	Placenta
21	chr4:2871200-2877400	Weak transcription	Thymus	Thymus
22	chr4:2871200-2881600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:2871200-2886000	Weak transcription	Aorta	Aorta
24	chr4:2871200-2896000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:2871200-2900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:2871400-2877400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:2871400-2877400	Weak transcription	Fetal Kidney	kidney
28	chr4:2871400-2879400	Weak transcription	Gastric	stomach
29	chr4:2871600-2877200	Weak transcription	Brain Germinal Matrix	brain
30	chr4:2871600-2877600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:2871600-2877600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:2871600-2880800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:2871800-2875200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:2871800-2876800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:2871800-2876800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:2871800-2877400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:2871800-2877800	Weak transcription	Fetal Brain Female	brain
38	chr4:2871800-2880400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:2872000-2876600	Weak transcription	Fetal Stomach	stomach
40	chr4:2872000-2877200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:2872200-2890800	Weak transcription	A549	lung
42	chr4:2872400-2876600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:2872400-2877600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:2872600-2875200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:2872600-2876000	Enhancers	Liver	Liver
46	chr4:2872600-2877800	Enhancers	Brain Hippocampus Middle	brain
47	chr4:2873000-2875400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:2873000-2875800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr4:2873200-2875200	Enhancers	Primary B cells from cord blood	blood
50	chr4:2873200-2875200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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