Variant report

Variant	rs11098987
Chromosome Location	chr4:129763599-129763600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129762106..129764642-chr4:129772413..129774661,2	K562	blood:
2	chr4:129730787..129735075-chr4:129762435..129766332,7	K562	blood:
3	chr4:129754977..129757198-chr4:129761484..129764208,2	K562	blood:
4	chr4:129730787..129732850-chr4:129762435..129765070,2	K562	blood:
5	chr4:129760081..129764752-chr4:129766854..129770363,4	K562	blood:

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[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11724119	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425618	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1648062	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs167618	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17013778	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2016294	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs318504	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs318505	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs318555	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318556	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975263	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975264	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975266	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975268	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975270	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55829553	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62317868	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833391	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6844446	0.85[EUR][1000 genomes];0.87[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
rs11098987	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129746800-129770200	Weak transcription	HMEC	breast
2	chr4:129747000-129766600	Weak transcription	NHEK	skin
3	chr4:129752400-129763800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:129753000-129766200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:129753200-129763800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:129753200-129767600	Weak transcription	Colonic Mucosa	Colon
7	chr4:129753400-129764000	Weak transcription	Fetal Brain Female	brain
8	chr4:129753400-129766000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:129753400-129767600	Weak transcription	Fetal Brain Male	brain
10	chr4:129753600-129767600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:129753600-129798600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:129753800-129770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:129753800-129795000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:129754400-129770600	Weak transcription	Fetal Kidney	kidney
15	chr4:129755400-129764800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:129756600-129763800	Weak transcription	Hela-S3	cervix
17	chr4:129756800-129763800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:129756800-129764200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:129757000-129764600	Weak transcription	Brain Angular Gyrus	brain
20	chr4:129757000-129770000	Weak transcription	Small Intestine	intestine
21	chr4:129757200-129763800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:129757200-129763800	Weak transcription	Brain Anterior Caudate	brain
23	chr4:129757200-129764000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:129757200-129764000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:129757200-129764200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:129757200-129764200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:129757200-129764200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:129757200-129764400	Weak transcription	HSMMtube	muscle
29	chr4:129757200-129764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:129757200-129765000	Weak transcription	Spleen	Spleen
31	chr4:129757200-129765200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:129757200-129768200	Weak transcription	Fetal Lung	lung
33	chr4:129757400-129763800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:129757400-129763800	Weak transcription	Brain Germinal Matrix	brain
35	chr4:129757400-129764200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:129757400-129764600	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:129757400-129765000	Weak transcription	Brain Substantia Nigra	brain
38	chr4:129757400-129765600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr4:129757400-129766000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:129757400-129766200	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:129758200-129763800	Weak transcription	NH-A	brain
42	chr4:129758400-129763600	Weak transcription	Fetal Intestine Large	intestine
43	chr4:129758400-129763800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr4:129759000-129763800	Weak transcription	Gastric	stomach
45	chr4:129759000-129763800	Weak transcription	NHLF	lung
46	chr4:129759000-129764600	Weak transcription	Stomach Mucosa	stomach
47	chr4:129759200-129763600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr4:129759400-129763800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:129759400-129763800	Weak transcription	HepG2	liver
50	chr4:129760000-129764000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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