Variant report

Variant	rs4693799
Chromosome Location	chr4:87915295-87915296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87912671..87915829-chr4:87926237..87929506,4	MCF-7	breast:
2	chr4:87907221..87909869-chr4:87913541..87915799,2	K562	blood:
3	chr4:87913434..87916324-chr4:87927780..87929757,3	MCF-7	breast:
4	chr4:87892847..87896142-chr4:87913687..87916404,3	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10003332	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10008600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10022960	0.92[ASN][1000 genomes]
rs1374936	0.83[ASN][1000 genomes]
rs1374937	0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1584345	0.90[CHB][hapmap]
rs168161	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1972969	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2053774	0.91[ASN][1000 genomes]
rs2272777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2594276	0.83[CHB][hapmap]
rs2705617	0.83[ASN][1000 genomes]
rs340627	0.97[ASN][1000 genomes]
rs340628	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340629	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340632	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs340635	1.00[ASN][1000 genomes]
rs340640	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340644	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340645	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340646	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340649	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340652	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4536897	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4693155	1.00[CHB][hapmap];1.00[JPT][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]
rs4693797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs58317309	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6531943	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531944	1.00[CHB][hapmap];1.00[JPT][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]
rs6531945	1.00[CHB][hapmap];0.88[JPT][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]
rs6531947	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815546	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6848056	0.92[ASN][1000 genomes]
rs6853011	0.92[ASN][1000 genomes]
rs72876089	0.89[EUR][1000 genomes]
rs73837575	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7685248	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs895740	0.83[ASN][1000 genomes]
rs965824	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4693799	Hs.480174	cis	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:87894600-87915600	Weak transcription	Lung	lung
5	chr4:87894600-87921000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:87895400-87920000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr4:87896200-87916000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:87896200-87919200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:87896800-87918800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:87897600-87915600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:87898200-87915400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:87899000-87915400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:87899000-87915400	Weak transcription	Left Ventricle	heart
14	chr4:87899000-87920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:87899000-87921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:87899200-87920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:87899200-87922800	Weak transcription	Osteobl	bone
18	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
19	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:87900000-87915600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:87900000-87924400	Weak transcription	NHEK	skin
22	chr4:87900200-87920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:87903200-87918800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:87903400-87915400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:87903600-87915400	Weak transcription	Thymus	Thymus
27	chr4:87903600-87915400	Weak transcription	Dnd41	blood
28	chr4:87903600-87919800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:87903600-87921000	Weak transcription	Primary T cells from cord blood	blood
30	chr4:87903800-87915600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:87903800-87919800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:87903800-87920000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:87904200-87926200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:87904400-87915800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:87904400-87920000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr4:87904600-87915800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:87904600-87917800	Weak transcription	Primary B cells from cord blood	blood
38	chr4:87904600-87921000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:87905800-87920200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:87907600-87920000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:87908800-87915400	Weak transcription	GM12878-XiMat	blood
42	chr4:87909600-87915600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:87910000-87915600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:87910000-87919000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:87910000-87921200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:87911800-87915400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:87911800-87915800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:87912800-87920600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:87913000-87916200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:87913000-87919400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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