Variant report

Variant	rs4241604
Chromosome Location	chr4:78074963-78074964
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	chr4:78074226-78075659	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78020522..78022856-chr4:78073841..78076321,2	MCF-7	breast:
2	chr4:77993925..77999822-chr4:78072652..78081114,32	MCF-7	breast:

Variant related genes	Relation type
CCNG2	TF binding region
RNU6-1187P	TF binding region
ENSG00000118816	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10025838	0.96[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1006042	0.84[GIH][hapmap]
rs11097704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11724432	0.86[JPT][hapmap]
rs11731592	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12504752	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12509168	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs12640093	0.96[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs28464714	0.87[ASN][1000 genomes]
rs28503908	0.86[JPT][hapmap]
rs4280759	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4302483	0.86[JPT][hapmap]
rs4365751	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382065	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4518274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4544732	0.86[JPT][hapmap]
rs4547817	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4558892	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4563522	0.91[EUR][1000 genomes]
rs4859473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859751	0.86[JPT][hapmap]
rs4859756	0.92[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs6532867	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532868	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532870	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532871	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6846698	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs6849124	0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6849534	0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7654920	0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4241604	CCNG2	cis	cerebellum	SCAN
rs4241604	PAQR3	cis	cerebellum	SCAN
rs4241604	PF4V1	cis	cerebellum	SCAN
rs4241604	TMPRSS2	trans	cerebellum	SCAN
rs4241604	BMP3	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78067800-78077600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:78068000-78076000	Weak transcription	HMEC	breast
3	chr4:78068200-78075200	Weak transcription	NHEK	skin
4	chr4:78068600-78075800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:78068600-78076600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:78069200-78077400	Weak transcription	HSMMtube	muscle
7	chr4:78069400-78076400	Weak transcription	Hela-S3	cervix
8	chr4:78071200-78077600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:78072000-78077400	Enhancers	Primary B cells from peripheral blood	blood
10	chr4:78072400-78077400	Enhancers	Fetal Thymus	thymus
11	chr4:78073200-78075800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr4:78073200-78076800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:78073200-78076800	Enhancers	Fetal Lung	lung
14	chr4:78073200-78077400	Enhancers	Primary T cells from cord blood	blood
15	chr4:78073200-78077400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr4:78073400-78075200	Enhancers	GM12878-XiMat	blood
17	chr4:78073400-78075600	Enhancers	Thymus	Thymus
18	chr4:78073400-78076800	Enhancers	Fetal Intestine Small	intestine
19	chr4:78073400-78077200	Enhancers	Fetal Intestine Large	intestine
20	chr4:78073600-78077000	Enhancers	Duodenum Mucosa	Duodenum
21	chr4:78073600-78077400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr4:78073600-78077600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr4:78073800-78076800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr4:78074000-78075200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:78074000-78075200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:78074000-78076200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:78074000-78076400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:78074000-78076400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:78074000-78076600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:78074000-78077000	Enhancers	Primary hematopoietic stem cells	blood
31	chr4:78074000-78077200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:78074000-78077400	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr4:78074200-78075200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:78074200-78075600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:78074200-78076000	Enhancers	Primary B cells from cord blood	blood
36	chr4:78074200-78076000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:78074200-78076200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:78074200-78076400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:78074200-78076400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:78074200-78076600	Weak transcription	Stomach Mucosa	stomach
41	chr4:78074200-78077200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:78074400-78075000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:78074400-78075400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:78074400-78075400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:78074400-78076000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:78074400-78076200	Weak transcription	Fetal Kidney	kidney
47	chr4:78074400-78076400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:78074400-78076400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:78074400-78076800	Weak transcription	Placenta	Placenta
50	chr4:78074600-78075400	Enhancers	Rectal Mucosa Donor 31	rectum

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