Variant report

Variant	rs318505
Chromosome Location	chr4:129808936-129808937
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10017436	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11098987	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11724119	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11731189	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1425618	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1648062	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs167618	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013778	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2016294	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318504	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs318555	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs318556	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4052	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4975263	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4975264	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4975266	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4975268	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4975270	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55829553	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62317868	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6833391	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6844446	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
3	nsv1026938	chr4:129770961-129936205	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv870175	chr4:129771718-129937945	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1026772	chr4:129773881-129936205	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv461637	chr4:129774375-129924977	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv595397	chr4:129774375-129924977	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv461638	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv595398	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1018994	chr4:129775612-129933968	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv1034996	chr4:129777825-129905255	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv537249	chr4:129777825-129905255	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv1022446	chr4:129778025-129905116	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv537250	chr4:129778025-129905116	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS 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
16	nsv1030296	chr4:129778025-129920680	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv537251	chr4:129778025-129920680	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
18	esv2830419	chr4:129785483-129905256	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
19	nsv533785	chr4:129785683-129857992	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a
20	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv1026722	chr4:129801602-129929219	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv537252	chr4:129801602-129929219	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs318505	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129779600-129809800	Weak transcription	Small Intestine	intestine
2	chr4:129789400-129811200	Weak transcription	Placenta	Placenta
3	chr4:129793200-129812200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:129793600-129812000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:129793600-129812200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:129793600-129812800	Weak transcription	Spleen	Spleen
7	chr4:129793600-129815400	Weak transcription	Fetal Lung	lung
8	chr4:129793600-129816800	Weak transcription	Lung	lung
9	chr4:129793600-129817200	Weak transcription	Psoas Muscle	Psoas
10	chr4:129793600-129825000	Weak transcription	Ovary	ovary
11	chr4:129793800-129811600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr4:129793800-129907200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:129794000-129809200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:129794000-129813400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:129794000-129814800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:129794200-129810800	Weak transcription	Fetal Brain Female	brain
17	chr4:129794200-129810800	Weak transcription	Right Ventricle	heart
18	chr4:129794200-129812000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:129794200-129815000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:129794200-129816800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr4:129794200-129824800	Weak transcription	Osteobl	bone
22	chr4:129794200-129829400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:129794400-129809400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:129794400-129811000	Weak transcription	Aorta	Aorta
25	chr4:129794400-129811200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:129794400-129811400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:129794400-129823800	Weak transcription	Left Ventricle	heart
28	chr4:129794400-129825600	Weak transcription	Gastric	stomach
29	chr4:129794400-129860200	Weak transcription	Thymus	Thymus
30	chr4:129795000-129809400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:129795000-129824600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:129795200-129813400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr4:129795400-129809600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:129795400-129810200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:129795400-129811200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:129795800-129811800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:129795800-129812200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:129796000-129809400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:129796000-129810800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:129796000-129810800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:129796000-129811400	Weak transcription	HSMM	muscle
42	chr4:129796200-129809800	Weak transcription	Dnd41	blood
43	chr4:129796800-129809400	Weak transcription	Primary T cells from cord blood	blood
44	chr4:129796800-129809600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr4:129796800-129809800	Weak transcription	Adipose Nuclei	Adipose
46	chr4:129796800-129811400	Weak transcription	NH-A	brain
47	chr4:129796800-129813200	Weak transcription	Liver	Liver
48	chr4:129797600-129809400	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:129798000-129809400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:129798000-129811000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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