Variant report

Variant	rs10017436
Chromosome Location	chr4:129737089-129737090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129382385..129384000-chr4:129736037..129738354,2	K562	blood:
2	chr4:129736742..129738918-chr4:129767515..129769516,2	K562	blood:
3	chr4:129736160..129738692-chr4:129755365..129757627,2	K562	blood:
4	chr4:129732370..129733941-chr4:129735604..129737176,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10032000	0.81[JPT][hapmap]
rs10518539	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs11098987	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11724119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11731189	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs13143771	0.87[JPT][hapmap]
rs1425618	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1648062	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1668289	0.80[JPT][hapmap]
rs167618	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17013778	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1993035	1.00[YRI][hapmap]
rs2016294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2162126	0.81[JPT][hapmap]
rs2217023	0.87[JPT][hapmap]
rs318502	0.81[JPT][hapmap]
rs318504	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318505	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318536	0.81[JPT][hapmap]
rs318543	0.81[JPT][hapmap]
rs318552	0.80[JPT][hapmap]
rs318555	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs318556	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4423892	0.85[YRI][hapmap]
rs4975263	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975264	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975268	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975274	0.81[JPT][hapmap]
rs55829553	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62317868	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6832138	1.00[YRI][hapmap]
rs6833391	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6835359	0.85[YRI][hapmap]
rs6844446	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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	nsv822717	chr4:129724785-129739862	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10017436	C4orf29	cis	cerebellum	SCAN
rs10017436	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs10017436	SCLT1	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734000-129738200	Weak transcription	Pancreas	Pancrea
2	chr4:129734000-129738400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:129734000-129740200	Weak transcription	Gastric	stomach
4	chr4:129734000-129740400	Weak transcription	Lung	lung
5	chr4:129734000-129741600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:129734200-129738000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:129734200-129738800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:129734200-129740000	Weak transcription	Left Ventricle	heart
9	chr4:129734200-129746200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:129734200-129746200	Weak transcription	Ovary	ovary
11	chr4:129734200-129746800	Weak transcription	Fetal Stomach	stomach
12	chr4:129734200-129747000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:129734400-129738000	Weak transcription	Right Atrium	heart
14	chr4:129734400-129739600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:129734400-129739600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:129734400-129739600	Weak transcription	Psoas Muscle	Psoas
17	chr4:129734400-129739600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr4:129734400-129740000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:129734400-129740400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:129734400-129740400	Weak transcription	Fetal Intestine Small	intestine
21	chr4:129734400-129740400	Weak transcription	NH-A	brain
22	chr4:129734400-129740800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:129734400-129742400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:129734400-129745600	Weak transcription	Fetal Intestine Large	intestine
25	chr4:129734400-129746000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:129734400-129746000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:129734400-129746200	Weak transcription	Fetal Muscle Leg	muscle
28	chr4:129734400-129751600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
30	chr4:129734600-129738400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:129734600-129739800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:129734600-129740000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:129734600-129740200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:129734600-129740200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:129734600-129740400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:129734600-129740800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:129734600-129743200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:129734600-129743800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:129734600-129743800	Weak transcription	NHEK	skin
40	chr4:129734600-129745600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:129734600-129746400	Weak transcription	Right Ventricle	heart
42	chr4:129735000-129737600	Weak transcription	Fetal Thymus	thymus
43	chr4:129735000-129738000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:129735000-129740000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:129735000-129740400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:129735000-129743200	Weak transcription	Adipose Nuclei	Adipose
47	chr4:129735000-129747000	Weak transcription	Primary B cells from cord blood	blood
48	chr4:129735200-129737200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr4:129735200-129738400	Weak transcription	NHDF-Ad	bronchial
50	chr4:129735200-129746400	Weak transcription	Stomach Smooth Muscle	stomach

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