Variant report

Variant	rs2016294
Chromosome Location	chr4:129766403-129766404
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129764059..129767011-chr4:129767338..129770023,2	MCF-7	breast:
2	chr4:129760081..129763027-chr4:129766274..129768354,2	K562	blood:
3	chr4:129760491..129763213-chr4:129764575..129766528,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10008927	0.88[JPT][hapmap]
rs10017436	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]
rs10518539	0.85[YRI][hapmap]
rs11098987	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11724119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11731189	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs1425618	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1648062	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs167618	0.87[CEU][hapmap];0.90[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17013778	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993035	1.00[YRI][hapmap]
rs318504	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs318505	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318555	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318556	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4423892	0.85[YRI][hapmap]
rs4975263	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975264	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975268	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975269	0.82[JPT][hapmap]
rs4975270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55829553	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317868	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6832138	1.00[YRI][hapmap]
rs6833391	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6835359	0.85[YRI][hapmap]
rs6844446	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6857659	0.82[JPT][hapmap]

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
rs2016294	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 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	chr4:129753200-129767600	Weak transcription	Colonic Mucosa	Colon
4	chr4:129753400-129767600	Weak transcription	Fetal Brain Male	brain
5	chr4:129753600-129767600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:129753600-129798600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:129753800-129770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:129753800-129795000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:129754400-129770600	Weak transcription	Fetal Kidney	kidney
10	chr4:129757000-129770000	Weak transcription	Small Intestine	intestine
11	chr4:129757200-129768200	Weak transcription	Fetal Lung	lung
12	chr4:129760400-129783400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:129761400-129767400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:129761400-129767400	Strong transcription	Osteobl	bone
15	chr4:129761400-129768000	Strong transcription	Primary B cells from cord blood	blood
16	chr4:129761600-129769000	Enhancers	Right Atrium	heart
17	chr4:129761600-129770800	Strong transcription	NHDF-Ad	bronchial
18	chr4:129761600-129779400	Strong transcription	Fetal Stomach	stomach
19	chr4:129761600-129782000	Strong transcription	Fetal Intestine Small	intestine
20	chr4:129761600-129785000	Strong transcription	Thymus	Thymus
21	chr4:129761800-129775000	Strong transcription	GM12878-XiMat	blood
22	chr4:129762000-129782800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr4:129762200-129773800	Strong transcription	Dnd41	blood
24	chr4:129762200-129775000	Strong transcription	Fetal Thymus	thymus
25	chr4:129762400-129771800	Strong transcription	K562	blood
26	chr4:129762400-129775000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:129762400-129775000	Strong transcription	HSMM	muscle
28	chr4:129762400-129784200	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr4:129762600-129775000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:129762600-129775400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:129762800-129767800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:129762800-129784200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:129763000-129768600	Weak transcription	Fetal Heart	heart
34	chr4:129763000-129774600	Strong transcription	Primary T cells from cord blood	blood
35	chr4:129763000-129783800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:129763000-129785800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:129763000-129787200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:129763200-129767800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:129763200-129768200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:129763200-129784000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:129763200-129784000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:129763400-129774800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:129763400-129784200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:129763600-129767800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:129763600-129774600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:129763600-129774800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr4:129763600-129774800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:129763600-129774800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:129763600-129777400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:129763600-129780400	Strong transcription	H1 Cell Line	embryonic stem cell

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