Variant report

Variant	rs7687562
Chromosome Location	chr4:129739899-129739900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129732203..129736510-chr4:129738670..129742463,5	MCF-7	breast:
2	chr4:129739255..129743318-chr4:129756229..129760124,4	K562	blood:
3	chr4:129730289..129733712-chr4:129739240..129742412,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10002332	0.90[JPT][hapmap]
rs10008927	0.92[CEU][hapmap];0.81[YRI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10032000	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12171333	0.92[JPT][hapmap]
rs12512715	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13120702	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13143771	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1648062	0.85[JPT][hapmap]
rs1668289	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1841259	0.86[ASN][1000 genomes]
rs1841260	0.88[ASN][1000 genomes]
rs2162126	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2198042	0.91[JPT][hapmap]
rs2217023	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs280603	0.91[JPT][hapmap]
rs3099899	0.92[JPT][hapmap]
rs3113407	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs318500	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318501	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318502	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318503	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318504	0.85[JPT][hapmap]
rs318513	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs318517	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318521	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs318536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs318543	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs318552	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs318556	0.86[JPT][hapmap]
rs4466058	0.85[JPT][hapmap]
rs4975265	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975267	0.91[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975269	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975274	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62317870	0.88[ASN][1000 genomes]
rs6817004	0.86[ASN][1000 genomes]
rs6834108	0.86[ASN][1000 genomes]
rs6847753	0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs6857659	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7655841	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7687562	LOC132321	cis	multi-tissue	Pritchard
rs7687562	C4orf33	cis	multi-tissue	Pritchard
rs7687562	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs7687562	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs7687562	C4orf33	cis	Artery Tibial	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734000-129740200	Weak transcription	Gastric	stomach
2	chr4:129734000-129740400	Weak transcription	Lung	lung
3	chr4:129734000-129741600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:129734200-129740000	Weak transcription	Left Ventricle	heart
5	chr4:129734200-129746200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:129734200-129746200	Weak transcription	Ovary	ovary
7	chr4:129734200-129746800	Weak transcription	Fetal Stomach	stomach
8	chr4:129734200-129747000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:129734400-129740000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:129734400-129740400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:129734400-129740400	Weak transcription	Fetal Intestine Small	intestine
12	chr4:129734400-129740400	Weak transcription	NH-A	brain
13	chr4:129734400-129740800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:129734400-129742400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:129734400-129745600	Weak transcription	Fetal Intestine Large	intestine
16	chr4:129734400-129746000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:129734400-129746000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:129734400-129746200	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:129734400-129751600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
21	chr4:129734600-129740000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:129734600-129740200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:129734600-129740200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:129734600-129740400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:129734600-129740800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:129734600-129743200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:129734600-129743800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:129734600-129743800	Weak transcription	NHEK	skin
29	chr4:129734600-129745600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:129734600-129746400	Weak transcription	Right Ventricle	heart
31	chr4:129735000-129740000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:129735000-129740400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:129735000-129743200	Weak transcription	Adipose Nuclei	Adipose
34	chr4:129735000-129747000	Weak transcription	Primary B cells from cord blood	blood
35	chr4:129735200-129746400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:129735400-129740000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:129735400-129740200	Weak transcription	NHLF	lung
38	chr4:129735400-129740600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:129735400-129744000	Weak transcription	Hela-S3	cervix
40	chr4:129735400-129748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:129735400-129752200	Weak transcription	Fetal Brain Female	brain
42	chr4:129735600-129740000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:129736000-129740000	Weak transcription	Small Intestine	intestine
44	chr4:129736400-129741800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr4:129736600-129740400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
46	chr4:129736600-129741200	Genic enhancers	A549	lung
47	chr4:129736600-129741800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
48	chr4:129736600-129744600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:129737000-129740800	Enhancers	Osteobl	bone
50	chr4:129737000-129741000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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