Variant report

Variant	rs4391704
Chromosome Location	chr1:46094236-46094237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46083627..46085575-chr1:46092823..46094633,2	K562	blood:
2	chr1:46093995..46096884-chr1:46099449..46101165,2	K562	blood:
3	chr1:46092930..46095558-chr1:46100346..46102809,2	MCF-7	breast:
4	chr1:46085809..46088151-chr1:46093251..46095018,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159592	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10430123	0.84[JPT][hapmap]
rs10430124	0.84[JPT][hapmap]
rs10749856	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10789467	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10789470	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs10890333	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs10890336	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs11211157	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs11211163	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs11211166	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11211178	0.81[CHB][hapmap]
rs11587650	0.84[EUR][1000 genomes]
rs12025621	0.85[EUR][1000 genomes]
rs12037459	0.82[CHB][hapmap]
rs12043945	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs12049027	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs12091503	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs12404197	0.83[EUR][1000 genomes]
rs1250	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs1547924	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2050376	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2088102	0.95[CEU][hapmap];0.94[CHB][hapmap]
rs2230657	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs2230658	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2230659	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2275085	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs28378621	0.85[EUR][1000 genomes]
rs28635845	0.85[EUR][1000 genomes]
rs28647556	0.88[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs28817701	0.89[JPT][hapmap]
rs28844317	0.86[EUR][1000 genomes]
rs2934857	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs2991975	0.88[CEU][hapmap]
rs2991985	0.95[EUR][1000 genomes]
rs2991986	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2991987	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2991989	0.80[CHB][hapmap]
rs2993263	0.81[CEU][hapmap]
rs3013594	0.87[EUR][1000 genomes]
rs3013595	0.91[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs3013596	0.90[EUR][1000 genomes]
rs3013597	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs3014210	0.89[CHB][hapmap]
rs3014216	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs3014218	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs3014238	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes]
rs3014239	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs3014242	0.89[CHB][hapmap]
rs3014243	0.87[EUR][1000 genomes]
rs3014247	0.86[EUR][1000 genomes]
rs4274104	0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs4353138	0.86[EUR][1000 genomes]
rs4431884	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs4468203	0.90[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes]
rs4559551	0.84[JPT][hapmap]
rs4564187	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4609469	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4626927	0.84[CEU][hapmap]
rs4660312	0.94[EUR][1000 genomes]
rs4660882	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes]
rs4660885	0.80[CEU][hapmap]
rs5021934	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes]
rs518216	0.89[CHB][hapmap]
rs6429576	0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs6656279	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes]
rs6671802	0.92[EUR][1000 genomes]
rs6697821	0.84[JPT][hapmap]
rs6703960	0.83[EUR][1000 genomes]
rs72688483	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
3	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
5	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs4391704	CCDC163P	cis	Nerve Tibial	GTEx
rs4391704	GPBP1L1	cis	Whole Blood	GTEx
rs4391704	CCDC163P	cis	Artery Tibial	GTEx
rs4391704	CCDC163P	cis	Thyroid	GTEx
rs4391704	CCDC163P	cis	Heart Left Ventricle	GTEx
rs4391704	CCDC163P	cis	Whole Blood	GTEx
rs4391704	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs4391704	CCDC163P	cis	Esophagus Mucosa	GTEx
rs4391704	GPBP1L1	cis	Lymphoblastoid	GTEx
rs4391704	CCDC163P	cis	Artery Aorta	GTEx
rs4391704	MAST2	cis	Artery Aorta	GTEx
rs4391704	MAST2	cis	Artery Tibial	GTEx
rs4391704	CCDC163P	cis	lung	GTEx
rs4391704	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs4391704	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs4391704	AKR1A1	cis	multi-tissue	Pritchard
rs4391704	CCDC163P	cis	Stomach	GTEx
rs4391704	Hs.396207	cis	multi-tissue	Pritchard
rs4391704	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs4391704	CCDC163P	cis	Esophagus Muscularis	GTEx
rs4391704	CCDC163P	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46052800-46099400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:46070000-46108200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:46071600-46105800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:46074800-46108200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:46077800-46112600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:46078200-46101200	Strong transcription	Thymus	Thymus
8	chr1:46078400-46100800	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:46078800-46101000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:46079000-46100600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:46079600-46094600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:46079800-46109800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:46083400-46095000	Weak transcription	Stomach Mucosa	stomach
14	chr1:46084400-46094800	Weak transcription	Fetal Kidney	kidney
15	chr1:46086000-46096000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:46087600-46129200	Strong transcription	Fetal Thymus	thymus
17	chr1:46088000-46094400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:46088200-46095200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:46088200-46110000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr1:46088600-46127400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:46088800-46113400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:46089000-46098600	Weak transcription	Fetal Heart	heart
23	chr1:46089000-46100600	Strong transcription	Fetal Stomach	stomach
24	chr1:46089000-46108800	Strong transcription	Osteobl	bone
25	chr1:46089000-46109400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:46089000-46109400	Strong transcription	Liver	Liver
27	chr1:46089000-46109600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:46089200-46108800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:46089200-46109800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:46089200-46110000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:46089400-46095200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:46089600-46126400	Strong transcription	Primary T cells from cord blood	blood
33	chr1:46089800-46094600	Strong transcription	Adipose Nuclei	Adipose
34	chr1:46089800-46127000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:46090000-46101200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:46090200-46109800	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:46091000-46100600	Strong transcription	Lung	lung
38	chr1:46091000-46108200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr1:46091000-46126400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:46091200-46098400	Strong transcription	Fetal Intestine Small	intestine
41	chr1:46091200-46100600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:46091200-46107600	Strong transcription	Fetal Intestine Large	intestine
43	chr1:46091200-46108400	Strong transcription	Placenta	Placenta
44	chr1:46091200-46108600	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr1:46091200-46108800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:46091200-46109000	Strong transcription	Rectal Smooth Muscle	rectum
47	chr1:46091200-46109800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:46091200-46120400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:46091200-46120800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:46091200-46127000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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