Variant report

Variant	rs6833391
Chromosome Location	chr4:129742066-129742067
allele	A/G
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	chr4:129729749..129732132-chr4:129741755..129744281,2	MCF-7	breast:
4	chr4:129730289..129733712-chr4:129739240..129742412,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10017436	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098987	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11724119	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1425618	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1648062	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs167618	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17013778	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016294	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs318504	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs318505	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318555	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318556	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975263	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975264	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975266	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975268	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975270	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55829553	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62317868	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844446	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6833391	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734200-129746200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:129734200-129746200	Weak transcription	Ovary	ovary
3	chr4:129734200-129746800	Weak transcription	Fetal Stomach	stomach
4	chr4:129734200-129747000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:129734400-129742400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:129734400-129745600	Weak transcription	Fetal Intestine Large	intestine
7	chr4:129734400-129746000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:129734400-129746000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:129734400-129746200	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:129734400-129751600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
12	chr4:129734600-129743200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:129734600-129743800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:129734600-129743800	Weak transcription	NHEK	skin
15	chr4:129734600-129745600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:129734600-129746400	Weak transcription	Right Ventricle	heart
17	chr4:129735000-129743200	Weak transcription	Adipose Nuclei	Adipose
18	chr4:129735000-129747000	Weak transcription	Primary B cells from cord blood	blood
19	chr4:129735200-129746400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:129735400-129744000	Weak transcription	Hela-S3	cervix
21	chr4:129735400-129748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:129735400-129752200	Weak transcription	Fetal Brain Female	brain
23	chr4:129736600-129744600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:129737000-129743200	Weak transcription	HUVEC	blood vessel
25	chr4:129737800-129744800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:129738400-129744400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr4:129738600-129749200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr4:129739000-129743000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:129739400-129744000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:129739800-129744000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:129740000-129746400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr4:129740200-129742400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:129740400-129742400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr4:129740400-129743800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr4:129740400-129749200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:129740600-129742600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:129740600-129742600	Genic enhancers	K562	blood
38	chr4:129740600-129742800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:129740600-129743200	Genic enhancers	HSMM	muscle
40	chr4:129740600-129746200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:129740600-129746200	Weak transcription	Right Atrium	heart
42	chr4:129740600-129746600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr4:129740600-129747000	Weak transcription	Thymus	Thymus
44	chr4:129740800-129743600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr4:129740800-129744000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:129740800-129746600	Weak transcription	Spleen	Spleen
47	chr4:129740800-129748000	Weak transcription	Liver	Liver
48	chr4:129741000-129742400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:129741000-129743200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:129741000-129743200	Weak transcription	NH-A	brain

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