Variant report

Variant	rs10026646
Chromosome Location	chr4:78089514-78089515
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78085870..78089937-chr4:78095551..78099001,4	MCF-7	breast:
2	chr4:78089133..78091106-chr4:78093966..78096748,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10009384	0.89[TSI][hapmap]
rs10016483	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10016676	0.84[AMR][1000 genomes]
rs10026129	0.89[TSI][hapmap]
rs10030957	0.87[TSI][hapmap]
rs10856957	0.89[TSI][hapmap]
rs11097730	0.89[TSI][hapmap]
rs11724432	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12498388	0.91[ASN][1000 genomes]
rs12500115	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs17397604	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28503908	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28540841	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28648488	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150106	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302483	0.95[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.96[MEX][hapmap]
rs4544732	0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4640692	0.91[ASN][1000 genomes]
rs4859474	0.85[ASN][1000 genomes]
rs4859751	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859753	0.89[TSI][hapmap]
rs4859755	0.89[TSI][hapmap]
rs55663411	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6849124	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs6849534	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs729240	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7438755	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7672053	0.88[ASN][1000 genomes]
rs7688769	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879500	chr4:78045960-78115334	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10026646	CXCL13	cis	cerebellum	SCAN
rs10026646	CCNG2	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78080000-78089800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:78080000-78092800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:78080000-78093400	Weak transcription	Right Ventricle	heart
4	chr4:78080200-78089800	Weak transcription	Aorta	Aorta
5	chr4:78080200-78094400	Weak transcription	Psoas Muscle	Psoas
6	chr4:78080400-78090800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:78080400-78091400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:78080400-78092400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr4:78080600-78089600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:78080600-78091800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:78080600-78091800	Strong transcription	Osteobl	bone
12	chr4:78080800-78089800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:78080800-78091000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:78080800-78091400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:78080800-78092400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:78081000-78090600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr4:78081200-78089800	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr4:78081200-78092000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:78081200-78092200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:78081200-78092400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:78081200-78092400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:78081200-78092400	Strong transcription	Placenta	Placenta
23	chr4:78081200-78092400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:78081200-78092600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:78081200-78092600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr4:78081200-78093000	Strong transcription	Primary hematopoietic stem cells	blood
27	chr4:78081200-78093600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:78081400-78092600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:78081600-78090200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:78081800-78091000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:78081800-78091800	Strong transcription	Adipose Nuclei	Adipose
32	chr4:78081800-78092400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:78082000-78089600	Strong transcription	Liver	Liver
34	chr4:78082000-78090000	Strong transcription	Fetal Muscle Leg	muscle
35	chr4:78082200-78092000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:78082600-78090600	Strong transcription	HSMMtube	muscle
37	chr4:78083000-78092000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:78083000-78092200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:78083000-78092400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr4:78083200-78090600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:78083200-78093600	Weak transcription	Small Intestine	intestine
42	chr4:78083400-78091800	Strong transcription	GM12878-XiMat	blood
43	chr4:78083400-78093000	Weak transcription	Fetal Heart	heart
44	chr4:78083400-78093600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:78083400-78095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:78083400-78095600	Weak transcription	HepG2	liver
47	chr4:78084200-78089800	Weak transcription	Gastric	stomach
48	chr4:78084200-78089800	Weak transcription	Pancreas	Pancrea
49	chr4:78084400-78091000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:78084400-78091200	Weak transcription	Fetal Intestine Small	intestine

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