Variant report

Variant	rs55829553
Chromosome Location	chr4:129755837-129755838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129731063..129734279-chr4:129754821..129757246,3	K562	blood:
2	chr4:129732985..129735463-chr4:129755056..129756818,2	MCF-7	breast:
3	chr4:129736160..129738692-chr4:129755365..129757627,2	K562	blood:
4	chr4:129754977..129757198-chr4:129761484..129764208,2	K562	blood:
5	chr4:129730975..129733896-chr4:129754884..129756961,2	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	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098987	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11724119	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1425618	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1648062	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs167618	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17013778	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016294	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs318504	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs318505	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318555	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318556	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975263	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975264	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975266	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975268	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975270	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317868	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833391	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6844446	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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
rs55829553	PHF17	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
2	chr4:129746600-129761800	Strong transcription	Dnd41	blood
3	chr4:129746800-129757000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:129746800-129770200	Weak transcription	HMEC	breast
5	chr4:129747000-129766600	Weak transcription	NHEK	skin
6	chr4:129747400-129756600	Weak transcription	Esophagus	oesophagus
7	chr4:129747400-129761600	Weak transcription	Placenta	Placenta
8	chr4:129748000-129761600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:129751600-129757200	Genic enhancers	Fetal Intestine Small	intestine
10	chr4:129752200-129756400	Weak transcription	Spleen	Spleen
11	chr4:129752400-129758000	Strong transcription	Primary T cells from cord blood	blood
12	chr4:129752400-129758600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:129752400-129763800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:129752600-129756800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:129752600-129757200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr4:129752600-129761800	Strong transcription	Fetal Thymus	thymus
17	chr4:129752800-129756000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:129752800-129756000	Weak transcription	Lung	lung
19	chr4:129752800-129756800	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr4:129752800-129758200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:129752800-129758200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:129752800-129760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:129753000-129756400	Weak transcription	HSMMtube	muscle
24	chr4:129753000-129756600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr4:129753000-129756800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:129753000-129757200	Strong transcription	Primary hematopoietic stem cells	blood
27	chr4:129753000-129757400	Strong transcription	Primary B cells from cord blood	blood
28	chr4:129753000-129758000	Strong transcription	Thymus	Thymus
29	chr4:129753000-129758600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:129753000-129761000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr4:129753000-129766200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:129753200-129756200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:129753200-129756200	Weak transcription	Brain Substantia Nigra	brain
34	chr4:129753200-129756200	Weak transcription	Gastric	stomach
35	chr4:129753200-129756200	Weak transcription	Left Ventricle	heart
36	chr4:129753200-129756200	Weak transcription	Right Atrium	heart
37	chr4:129753200-129756200	Strong transcription	NHLF	lung
38	chr4:129753200-129756400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:129753200-129756400	Weak transcription	Brain Germinal Matrix	brain
40	chr4:129753200-129756400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr4:129753200-129756800	Strong transcription	HUVEC	blood vessel
42	chr4:129753200-129759000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:129753200-129759200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:129753200-129759200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:129753200-129763800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:129753200-129767600	Weak transcription	Colonic Mucosa	Colon
47	chr4:129753400-129756000	Strong transcription	Fetal Muscle Leg	muscle
48	chr4:129753400-129756200	Weak transcription	Fetal Lung	lung
49	chr4:129753400-129756200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr4:129753400-129756600	Weak transcription	Brain Angular Gyrus	brain

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