Variant report

Variant	rs6547700
Chromosome Location	chr2:86851598-86851599
allele	A/C
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	E2F6	chr2:86849947-86851694	K562	blood:	n/a	chr2:86851018-86851028 chr2:86851097-86851108 chr2:86851049-86851061 chr2:86850621-86850631 chr2:86850454-86850463
2	MXI1	chr2:86848131-86851749	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr2:86850018-86851759	HepG2	liver:	n/a	n/a
4	TEAD4	chr2:86850722-86851613	K562	blood:	n/a	n/a
5	POLR2A	chr2:86849599-86851652	Raji	blood:	n/a	n/a
6	POLR2A	chr2:86849323-86851610	MCF10A-Er-Src	breast:	n/a	n/a
7	E2F6	chr2:86850546-86851727	H1-hESC	embryonic stem cell:	n/a	chr2:86851018-86851028 chr2:86851097-86851108 chr2:86851049-86851061 chr2:86850621-86850631
8	MAX	chr2:86849822-86851617	A549	lung:	n/a	n/a
9	CBX3	chr2:86850885-86851750	K562	blood:	n/a	n/a
10	MAX	chr2:86849834-86851630	K562	blood:	n/a	n/a
11	MXI1	chr2:86849402-86851680	IMR90	lung:	n/a	n/a
12	POLR2A	chr2:86849667-86851619	K562	blood:	n/a	n/a
13	MAX	chr2:86849670-86851716	HepG2	liver:	n/a	n/a
14	E2F6	chr2:86849788-86851821	A549	lung:	n/a	chr2:86851018-86851028 chr2:86851097-86851108 chr2:86851049-86851061 chr2:86850621-86850631 chr2:86850454-86850463
15	RUNX3	chr2:86850582-86851608	GM12878	blood:	n/a	n/a
16	MAX	chr2:86849870-86851716	HepG2	liver:	n/a	n/a
17	MAX	chr2:86850549-86851692	HCT-116	colon:	n/a	n/a
18	MAX	chr2:86849914-86851618	MCF-7	breast:	n/a	n/a
19	MAX	chr2:86849886-86851610	NB4	blood:	n/a	n/a
20	POLR2A	chr2:86849595-86851623	MCF-7	breast:	n/a	n/a
21	MAX	chr2:86850670-86851603	H1-hESC	embryonic stem cell:	n/a	n/a
22	E2F6	chr2:86850529-86851678	H1-hESC	embryonic stem cell:	n/a	chr2:86851018-86851028 chr2:86851097-86851108 chr2:86851049-86851061 chr2:86850621-86850631
23	MAX	chr2:86849698-86851784	A549	lung:	n/a	n/a
24	MAX	chr2:86850674-86851609	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F6	chr2:86851326-86851618	K562	blood:	n/a	n/a
26	POLR2A	chr2:86849580-86851651	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86849761..86852664-chr2:86946875..86949825,4	MCF-7	breast:
2	chr2:86667874..86671580-chr2:86848738..86852940,5	K562	blood:
3	chr2:86676152..86678942-chr2:86849820..86852421,2	MCF-7	breast:
4	chr2:86849205..86851980-chr4:103788532..103791480,2	MCF-7	breast:
5	chr2:86850777..86851624-chr8:145550290..145550908,2	HCT-116	colon:
6	chr2:86850136..86852379-chr2:86973884..86976847,2	K562	blood:
7	chr2:86848500..86851973-chr2:86945425..86949651,4	MCF-7	breast:
8	chr2:86839004..86842325-chr2:86847581..86852030,6	MCF-7	breast:
9	chr2:86669498..86671776-chr2:86849448..86851643,2	MCF-7	breast:
10	chr2:86787885..86791617-chr2:86846945..86852237,10	MCF-7	breast:

Variant related genes	Relation type
RNF103	TF binding region
RNF103-CHMP3	TF binding region
ENSG00000185000	Chromatin interaction
ENSG00000115561	Chromatin interaction
ENSG00000228363	Chromatin interaction
ENSG00000249884	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000153561	Chromatin interaction
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10185085	0.87[CHD][hapmap]
rs1036940	0.87[CHD][hapmap]
rs11127042	0.87[CHD][hapmap]
rs11127047	0.80[GIH][hapmap]
rs12623509	0.89[GIH][hapmap]
rs12714185	0.87[CHD][hapmap]
rs12714187	0.87[CHD][hapmap]
rs12995117	0.87[CHD][hapmap]
rs13034615	0.82[GIH][hapmap]
rs1629293	0.89[CEU][hapmap];0.83[GIH][hapmap]
rs2030259	0.87[CHD][hapmap]
rs2044230	0.87[CHD][hapmap]
rs2120340	0.98[ASN][1000 genomes]
rs218060	1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap]
rs308901	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs308902	0.96[CEU][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs308903	0.96[CEU][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs308907	1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap]
rs308910	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs308911	0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs308914	0.89[CEU][hapmap];0.83[GIH][hapmap]
rs396354	1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap]
rs422240	0.89[CEU][hapmap];0.85[GIH][hapmap]
rs433655	0.81[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap]
rs4832046	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4832289	0.87[CHD][hapmap]
rs4832294	0.87[CHD][hapmap]
rs6714826	0.87[CHD][hapmap]
rs683139	1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs7557796	0.80[GIH][hapmap]
rs7574389	0.87[CHD][hapmap]
rs966477	0.87[CHD][hapmap];0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3498261	chr2:86849516-86851839	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
5	esv3498262	chr2:86849516-86851839	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
6	esv3404473	chr2:86849666-86852214	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
7	nsv436305	chr2:86849862-86854021	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6547700	PTCD3	cis	cerebellum	SCAN
rs6547700	MAT2A	cis	parietal	SCAN
rs6547700	RMND5A	cis	cerebellum	SCAN
rs6547700	VPS24	cis	parietal	SCAN
rs6547700	IMMT	cis	cerebellum	SCAN
rs6547700	POLR1A	cis	cerebellum	SCAN
rs6547700	RNF103	cis	cerebellum	SCAN
rs6547700	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86847400-86851600	Active TSS	Right Ventricle	heart
2	chr2:86848000-86851600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:86848000-86851600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:86848200-86851600	Active TSS	Aorta	Aorta
5	chr2:86848200-86851600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:86848200-86851600	Active TSS	NH-A	brain
7	chr2:86848400-86851600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:86848400-86851600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:86848400-86851600	Active TSS	Fetal Muscle Trunk	muscle
10	chr2:86848400-86851600	Active TSS	Rectal Smooth Muscle	rectum
11	chr2:86849600-86851600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr2:86850200-86851600	Active TSS	Primary B cells from cord blood	blood
13	chr2:86851000-86851600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:86851000-86851600	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr2:86851000-86851600	Flanking Active TSS	HUVEC	blood vessel
16	chr2:86851000-86854800	Weak transcription	Gastric	stomach
17	chr2:86851000-86854800	Weak transcription	Small Intestine	intestine
18	chr2:86851000-86856400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:86851000-86860400	Weak transcription	Lung	lung
20	chr2:86851200-86851600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr2:86851200-86851600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:86851200-86851600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:86851200-86851600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:86851200-86851600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:86851200-86851600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:86851200-86851600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr2:86851200-86851600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr2:86851200-86851600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr2:86851200-86851600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr2:86851200-86851600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr2:86851200-86851600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:86851200-86851600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr2:86851200-86851600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:86851200-86851600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr2:86851200-86851600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:86851200-86851600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:86851200-86851600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr2:86851200-86851600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr2:86851200-86851600	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr2:86851200-86851600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr2:86851200-86851600	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr2:86851200-86851600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr2:86851200-86851600	Enhancers	Fetal Brain Male	brain
44	chr2:86851200-86851600	Flanking Active TSS	Fetal Heart	heart
45	chr2:86851200-86851600	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr2:86851200-86851600	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr2:86851200-86851600	Flanking Active TSS	Fetal Kidney	kidney
48	chr2:86851200-86851600	Flanking Active TSS	Fetal Lung	lung
49	chr2:86851200-86851600	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr2:86851200-86851600	Enhancers	Placenta Amnion	Placenta Amnion

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