Variant report

Variant	rs6849534
Chromosome Location	chr4:78073655-78073656
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr4:78073623-78073950	T-47D	breast:	n/a	n/a
2	GATA3	chr4:78073577-78073980	T-47D	breast:	n/a	n/a
3	GATA3	chr4:78073594-78073976	T-47D	breast:	n/a	n/a
4	KAP1	chr4:78073320-78073953	HEK293	kidney:	n/a	n/a
5	KAP1	chr4:78073405-78073919	U2OS	brain:	n/a	n/a
6	ESR1	chr4:78073597-78073976	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr4:78073395-78074077	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr4:78073491-78074135	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:77993925..77999822-chr4:78072652..78081114,32	MCF-7	breast:
2	chr4:78066334..78068831-chr4:78072502..78074956,2	K562	blood:
3	chr4:78067084..78069572-chr4:78071831..78074311,3	MCF-7	breast:
4	chr4:77995396..77998013-chr4:78072245..78073774,2	MCF-7	breast:

No data

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

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10016483	0.84[ASN][1000 genomes]
rs10016676	0.83[ASN][1000 genomes]
rs10025838	0.80[CEU][hapmap]
rs10026646	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs11097704	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap]
rs11724432	0.91[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12498388	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12500115	0.82[JPT][hapmap]
rs12504752	0.86[JPT][hapmap]
rs12509168	0.80[CEU][hapmap]
rs12640093	0.80[CEU][hapmap]
rs17397604	0.86[ASN][1000 genomes]
rs28503908	0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4150106	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs4241604	0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4280759	0.80[CEU][hapmap]
rs4302483	0.82[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4518274	0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4544732	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4547817	0.80[CEU][hapmap]
rs4640692	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859473	0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4859474	0.90[ASN][1000 genomes]
rs4859751	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4859752	0.82[JPT][hapmap]
rs4859756	0.84[CEU][hapmap]
rs55663411	0.86[ASN][1000 genomes]
rs6849124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729240	0.82[ASN][1000 genomes]
rs7438755	0.90[ASN][1000 genomes]
rs7672053	0.87[ASN][1000 genomes]
rs7688769	0.86[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
rs6849534	CCNG2	cis	cerebellum	SCAN
rs6849534	CXCL13	cis	cerebellum	SCAN

Chromatin state (count:52 , 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	chr4:78068200-78073800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:78068200-78075200	Weak transcription	NHEK	skin
5	chr4:78068600-78075800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:78068600-78076600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:78068800-78074000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:78068800-78074600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:78069200-78074000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:78069200-78077400	Weak transcription	HSMMtube	muscle
11	chr4:78069400-78073800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:78069400-78074200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:78069400-78076400	Weak transcription	Hela-S3	cervix
14	chr4:78070000-78074000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr4:78071200-78073800	Weak transcription	Small Intestine	intestine
16	chr4:78071200-78077600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:78072000-78077400	Enhancers	Primary B cells from peripheral blood	blood
18	chr4:78072400-78077400	Enhancers	Fetal Thymus	thymus
19	chr4:78072600-78074800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:78073200-78074000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr4:78073200-78075800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr4:78073200-78076800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:78073200-78076800	Enhancers	Fetal Lung	lung
24	chr4:78073200-78077400	Enhancers	Primary T cells from cord blood	blood
25	chr4:78073200-78077400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr4:78073400-78073800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr4:78073400-78074000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:78073400-78074000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr4:78073400-78074200	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr4:78073400-78074400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr4:78073400-78074400	Enhancers	Fetal Kidney	kidney
32	chr4:78073400-78074400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr4:78073400-78075200	Enhancers	GM12878-XiMat	blood
34	chr4:78073400-78075600	Enhancers	Thymus	Thymus
35	chr4:78073400-78076800	Enhancers	Fetal Intestine Small	intestine
36	chr4:78073400-78077200	Enhancers	Fetal Intestine Large	intestine
37	chr4:78073600-78073800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:78073600-78073800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr4:78073600-78074000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:78073600-78074200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:78073600-78074200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:78073600-78074200	Enhancers	Stomach Mucosa	stomach
43	chr4:78073600-78074400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:78073600-78074400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:78073600-78074400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr4:78073600-78074400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:78073600-78074400	Enhancers	Placenta	Placenta
48	chr4:78073600-78074800	Enhancers	Fetal Muscle Leg	muscle
49	chr4:78073600-78074800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr4:78073600-78077000	Enhancers	Duodenum Mucosa	Duodenum

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