Variant report

Variant	rs12645173
Chromosome Location	chr4:90036099-90036100
allele	A/G
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	POLR2A	chr4:90032368-90036875	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:90035789-90036849	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:90032629-90036890	K562	blood:	n/a	n/a
4	POLR2A	chr4:90031723-90036966	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90032004..90034943-chr4:90035415..90038647,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270720	TF binding region
FAM13A	TF binding region
ENSG00000138640	Chromatin interaction
ENSG00000180346	Chromatin interaction
ENSG00000271359	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10001420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10028121	1.00[JPT][hapmap]
rs10033476	1.00[CHB][hapmap]
rs10433881	0.96[ASN][1000 genomes]
rs11734924	1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs12647095	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12649875	0.96[ASN][1000 genomes]
rs13105546	0.96[ASN][1000 genomes]
rs13133608	0.96[ASN][1000 genomes]
rs13138927	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355836	0.85[ASN][1000 genomes]
rs1355837	0.85[ASN][1000 genomes]
rs1398937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1398938	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1398939	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1398941	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1398943	0.85[ASN][1000 genomes]
rs1513811	0.85[ASN][1000 genomes]
rs1513812	0.85[ASN][1000 genomes]
rs1513823	0.85[ASN][1000 genomes]
rs1533288	0.82[ASN][1000 genomes]
rs1533289	0.85[ASN][1000 genomes]
rs1533294	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1708659	0.85[ASN][1000 genomes]
rs1708671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1708672	0.81[ASN][1000 genomes]
rs1708673	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1708683	0.85[ASN][1000 genomes]
rs1795735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1795737	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1795740	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1828735	0.85[ASN][1000 genomes]
rs1996139	0.85[ASN][1000 genomes]
rs2102650	0.93[ASN][1000 genomes]
rs2670618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2670619	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2670620	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2670627	0.85[ASN][1000 genomes]
rs2670628	0.85[ASN][1000 genomes]
rs2704580	0.81[ASN][1000 genomes]
rs2704585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2704592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2869989	0.93[ASN][1000 genomes]
rs28718401	0.85[ASN][1000 genomes]
rs2904264	0.93[ASN][1000 genomes]
rs4325981	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693985	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4693987	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532100	0.85[ASN][1000 genomes]
rs6532113	0.96[ASN][1000 genomes]
rs6823241	0.96[ASN][1000 genomes]
rs6826482	0.93[ASN][1000 genomes]
rs6834297	0.85[ASN][1000 genomes]
rs6843986	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6845264	0.93[ASN][1000 genomes]
rs6846010	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7657630	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs8180333	0.85[ASN][1000 genomes]
rs9307063	0.96[ASN][1000 genomes]
rs938265	0.85[ASN][1000 genomes]
rs938267	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12645173	SPARCL1	cis	parietal	SCAN
rs12645173	TIGD2	cis	brain	BrainEAC
rs12645173	TIGD2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90036400	Weak transcription	HUVEC	blood vessel
4	chr4:90033600-90038400	Weak transcription	Psoas Muscle	Psoas
5	chr4:90033600-90039000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:90033600-90039000	Weak transcription	Lung	lung
7	chr4:90033600-90040800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:90033600-90043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:90033600-90045600	Weak transcription	Esophagus	oesophagus
10	chr4:90033600-90045600	Weak transcription	Pancreas	Pancrea
11	chr4:90033600-90049200	Weak transcription	Gastric	stomach
12	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
13	chr4:90033800-90036200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:90033800-90037600	Weak transcription	Fetal Thymus	thymus
15	chr4:90033800-90037600	Weak transcription	HSMM	muscle
16	chr4:90033800-90042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:90034000-90036400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:90034000-90037000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:90034000-90037000	Weak transcription	Fetal Lung	lung
20	chr4:90034000-90038400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:90034000-90038800	Weak transcription	Fetal Kidney	kidney
22	chr4:90034000-90039000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:90034000-90040400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:90034000-90040400	Weak transcription	NH-A	brain
25	chr4:90034000-90040800	Weak transcription	Osteobl	bone
26	chr4:90034000-90041600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:90034000-90042400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:90034000-90044000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:90034200-90038400	Weak transcription	Fetal Brain Male	brain
30	chr4:90034200-90040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:90034200-90040800	Weak transcription	NHDF-Ad	bronchial
32	chr4:90034200-90041000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:90034400-90036600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:90034400-90039000	Weak transcription	Dnd41	blood
36	chr4:90034400-90043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
38	chr4:90034600-90036200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:90034600-90037000	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr4:90034600-90040400	Weak transcription	HMEC	breast
41	chr4:90034600-90041600	Weak transcription	Fetal Intestine Large	intestine
42	chr4:90034600-90042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:90034800-90039200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:90034800-90040400	Weak transcription	NHEK	skin
45	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:90035000-90037600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:90035000-90043600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:90035200-90042600	Weak transcription	Fetal Intestine Small	intestine
49	chr4:90035200-90042600	Weak transcription	K562	blood
50	chr4:90035400-90037200	Weak transcription	A549	lung

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