Variant report

Variant	rs6857659
Chromosome Location	chr4:129763370-129763371
allele	G/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: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10008927	1.00[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10032000	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs12512715	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13120702	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13143771	0.81[CHD][hapmap];0.80[JPT][hapmap]
rs1668289	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1841260	0.80[ASN][1000 genomes]
rs2016294	0.82[JPT][hapmap]
rs2162126	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2217023	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099899	0.81[JPT][hapmap]
rs3113407	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs318500	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs318501	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs318502	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs318503	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs318513	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs318517	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318521	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs318536	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs318543	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap]
rs318552	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4975265	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4975267	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975270	0.82[JPT][hapmap]
rs4975274	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62317870	0.80[ASN][1000 genomes]
rs6847753	0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs7687562	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]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6857659	C4orf33	cis	multi-tissue	Pritchard
rs6857659	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs6857659	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs6857659	C4orf33	cis	Artery Tibial	GTEx
rs6857659	C4orf33	cis	lymphoblastoid	seeQTL
rs6857659	SCLT1	cis	cerebellum	SCAN
rs6857659	LOC132321	cis	multi-tissue	Pritchard

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	chr4:129757400-129763400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:129757400-129763800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:129757400-129763800	Weak transcription	Brain Germinal Matrix	brain
36	chr4:129757400-129764200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:129757400-129764600	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:129757400-129765000	Weak transcription	Brain Substantia Nigra	brain
39	chr4:129757400-129765600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr4:129757400-129766000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:129757400-129766200	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:129758200-129763800	Weak transcription	NH-A	brain
43	chr4:129758400-129763600	Weak transcription	Fetal Intestine Large	intestine
44	chr4:129758400-129763800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr4:129759000-129763800	Weak transcription	Gastric	stomach
46	chr4:129759000-129763800	Weak transcription	NHLF	lung
47	chr4:129759000-129764600	Weak transcription	Stomach Mucosa	stomach
48	chr4:129759200-129763600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr4:129759400-129763800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:129759400-129763800	Weak transcription	HepG2	liver

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