Variant report

Variant	rs17550470
Chromosome Location	chr5:146778867-146778868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr5:146778630-146778898	SH-SY5Y	brain:	n/a	n/a
2	EP300	chr5:146778477-146778917	SK-N-SH_RA	brain:	n/a	n/a
3	RAD21	chr5:146778504-146778883	SK-N-SH_RA	brain:	n/a	n/a
4	TCF12	chr5:146778192-146779069	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr5:146778344-146778919	SK-N-SH	brain:	n/a	n/a
6	EP300	chr5:146778515-146778940	SK-N-SH_RA	brain:	n/a	n/a
7	POLR2A	chr5:146778855-146778915	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr5:146778447-146778959	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:146777402..146779384-chr5:146780216..146783156,2	MCF-7	breast:
2	chr5:146777823..146779953-chr5:146786384..146788173,2	K562	blood:

Variant related genes	Relation type
ENSG00000272239	TF binding region
ENSG00000272239	Chromatin interaction
ENSG00000113657	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10042993	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10515586	0.84[MEX][hapmap];0.87[TSI][hapmap]
rs10515587	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17484444	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17548933	0.84[MEX][hapmap]
rs17550902	0.86[TSI][hapmap]
rs3805535	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6866421	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6877045	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6877057	0.94[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72833326	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17550470	SPINK6	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146762800-146783400	Weak transcription	Pancreas	Pancrea
2	chr5:146762800-146784200	Weak transcription	Colonic Mucosa	Colon
3	chr5:146767400-146782200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:146767800-146796600	Strong transcription	Brain Germinal Matrix	brain
5	chr5:146768000-146784000	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:146768600-146783400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:146769000-146783000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:146769400-146800600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:146769800-146810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:146770000-146800600	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr5:146770200-146784800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:146770200-146805200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:146770200-146810800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:146770400-146779000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:146770400-146783000	Strong transcription	Fetal Muscle Leg	muscle
16	chr5:146770400-146796600	Strong transcription	Fetal Brain Female	brain
17	chr5:146770400-146800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:146770600-146781600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr5:146770600-146782000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:146770600-146782800	Weak transcription	Fetal Heart	heart
21	chr5:146770600-146783200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr5:146770600-146783400	Strong transcription	Fetal Stomach	stomach
23	chr5:146770600-146798200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:146770600-146800400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:146771000-146781600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:146771600-146786600	Weak transcription	Gastric	stomach
27	chr5:146771800-146780800	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr5:146771800-146782000	Strong transcription	NH-A	brain
29	chr5:146772000-146781400	Strong transcription	Colon Smooth Muscle	Colon
30	chr5:146772000-146782600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:146772400-146783800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:146772600-146779800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:146772600-146781400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:146772800-146782400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:146772800-146783400	Weak transcription	Brain Substantia Nigra	brain
36	chr5:146772800-146795600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:146773400-146781000	Weak transcription	Psoas Muscle	Psoas
38	chr5:146773400-146784000	Weak transcription	Fetal Brain Male	brain
39	chr5:146773600-146788200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:146773600-146800600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:146774000-146799400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr5:146774200-146796800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr5:146774400-146783400	Weak transcription	HMEC	breast
44	chr5:146774600-146780000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr5:146774600-146783200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:146774600-146784200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:146774800-146780000	Strong transcription	Osteobl	bone
48	chr5:146774800-146782400	Weak transcription	HSMMtube	muscle
49	chr5:146775000-146779000	Strong transcription	Fetal Intestine Large	intestine
50	chr5:146775400-146780000	Weak transcription	Fetal Intestine Small	intestine

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