Variant report

Variant	rs17079910
Chromosome Location	chr3:48057147-48057148
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:91363406..91364175-chr3:48057111..48057623,2	MCF-7	breast:
2	chr3:48055864..48058624-chr3:48128858..48131357,3	MCF-7	breast:
3	chr3:48054963..48058951-chr3:48128022..48131548,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047849	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11918619	0.80[AMR][1000 genomes]
rs11926049	0.87[AMR][1000 genomes]
rs1380053	0.90[CHB][hapmap]
rs17290686	0.82[AMR][1000 genomes]
rs17498376	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes]
rs2306794	0.83[AMR][1000 genomes]
rs3731532	0.80[CHB][hapmap]
rs3772398	0.89[AMR][1000 genomes]
rs4364189	0.80[AMR][1000 genomes]
rs4858867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4858869	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4858870	0.89[AMR][1000 genomes]
rs4858883	0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs7431111	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	esv3335628	chr3:48010796-48074001	Weak transcription Enhancers Strong transcription Genic enhancers 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
10	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17079910	PTCHD2	trans	lymphoblastoid	seeQTL
rs17079910	KLHL18	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48003800-48060600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:48018000-48057200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:48027200-48063600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:48029200-48057400	Weak transcription	Spleen	Spleen
5	chr3:48035400-48057400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:48036000-48057200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:48040400-48062200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:48041000-48057200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:48043800-48075200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:48043800-48075200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:48048000-48059400	Weak transcription	Lung	lung
12	chr3:48050400-48057400	Weak transcription	Right Ventricle	heart
13	chr3:48051200-48057200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:48051200-48057200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:48051200-48128000	Weak transcription	Primary B cells from cord blood	blood
16	chr3:48051600-48058200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:48051600-48059000	Enhancers	Fetal Thymus	thymus
18	chr3:48051600-48065000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:48052200-48058600	Enhancers	Brain Angular Gyrus	brain
20	chr3:48052600-48058000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr3:48053000-48057200	Enhancers	HSMMtube	muscle
22	chr3:48053000-48057400	Weak transcription	Fetal Brain Male	brain
23	chr3:48053000-48059200	Enhancers	HepG2	liver
24	chr3:48053000-48061400	Enhancers	Thymus	Thymus
25	chr3:48053200-48057400	Enhancers	Fetal Kidney	kidney
26	chr3:48053200-48059400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:48053200-48059800	Enhancers	Colon Smooth Muscle	Colon
28	chr3:48053400-48058600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:48053400-48058600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:48053400-48058800	Enhancers	Duodenum Mucosa	Duodenum
31	chr3:48053400-48059400	Enhancers	NHDF-Ad	bronchial
32	chr3:48053600-48057600	Weak transcription	Aorta	Aorta
33	chr3:48053600-48058600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:48053600-48058800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:48053600-48060400	Enhancers	Fetal Heart	heart
36	chr3:48053600-48075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:48053800-48057200	Enhancers	HSMM	muscle
38	chr3:48053800-48057400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:48053800-48058400	Enhancers	Brain Cingulate Gyrus	brain
40	chr3:48053800-48059200	Enhancers	Osteobl	bone
41	chr3:48054000-48058400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:48054000-48059200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:48054200-48057200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:48054200-48059000	Enhancers	K562	blood
45	chr3:48054600-48059000	Enhancers	HUVEC	blood vessel
46	chr3:48054800-48057200	Enhancers	A549	lung
47	chr3:48054800-48059000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr3:48055000-48058000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr3:48055000-48058000	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr3:48055000-48058400	Enhancers	Liver	Liver

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