Variant report

Variant	rs7244678
Chromosome Location	chr18:11997197-11997198
allele	C/T
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	chr18:11996749-11997248	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr18:11993291-11997275	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr18:11996624-11997347	HepG2	liver:	n/a	n/a
4	POLR2A	chr18:11996956-11997304	HepG2	liver:	n/a	n/a
5	POLR2A	chr18:11994160-11997305	HL-60	blood:	n/a	n/a
6	POLR2A	chr18:11997039-11997232	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr18:11993400-11998536	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr18:11996821-11997231	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:11978568..11983192-chr18:11993805..11998306,5	MCF-7	breast:

Variant related genes	Relation type
IMPA2	TF binding region
ENSG00000266955	TF binding region
ENSG00000141401	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11545506	0.93[ASW][hapmap];0.80[CHB][hapmap];0.90[LWK][hapmap];0.80[MKK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs11660567	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs16976887	0.95[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs28475846	0.88[ASN][1000 genomes]
rs28499558	0.88[ASN][1000 genomes]
rs28509217	0.88[ASN][1000 genomes]
rs28548932	0.88[ASN][1000 genomes]
rs4239304	0.89[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs56364728	0.88[ASN][1000 genomes]
rs57967783	0.88[ASN][1000 genomes]
rs58556096	0.85[ASN][1000 genomes]
rs59796048	0.88[ASN][1000 genomes]
rs59889312	0.88[ASN][1000 genomes]
rs604420	0.88[CHB][hapmap]
rs6505700	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6505701	0.88[ASN][1000 genomes]
rs653074	0.90[CHB][hapmap]
rs663591	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs67450563	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67932171	0.88[ASN][1000 genomes]
rs7230346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7240032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72871698	0.88[ASN][1000 genomes]
rs72871700	0.88[ASN][1000 genomes]
rs72871702	0.88[ASN][1000 genomes]
rs72873509	0.88[ASN][1000 genomes]
rs72873510	0.88[ASN][1000 genomes]
rs72873549	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7407928	0.88[ASN][1000 genomes]
rs7506045	0.95[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs8095694	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs873085	0.85[CHB][hapmap]
rs9973177	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
2	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
3	chr18:11991000-11999200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr18:11993200-11998000	Enhancers	Stomach Mucosa	stomach
5	chr18:11993200-11998400	Enhancers	Fetal Muscle Trunk	muscle
6	chr18:11993400-11999400	Enhancers	Fetal Muscle Leg	muscle
7	chr18:11993400-12016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr18:11994400-11997600	Enhancers	Colonic Mucosa	Colon
9	chr18:11995000-11999200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr18:11995400-11998400	Enhancers	Brain Hippocampus Middle	brain
11	chr18:11995400-11999200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr18:11995400-12001800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:11995600-11998200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr18:11995600-11998600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr18:11995600-11998800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr18:11995600-11999000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr18:11995600-11999000	Weak transcription	Fetal Brain Female	brain
18	chr18:11995600-11999200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:11995600-11999400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr18:11995600-12014400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr18:11995800-11997400	Genic enhancers	Hela-S3	cervix
22	chr18:11995800-11999000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr18:11995800-11999400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr18:11996000-11997600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr18:11996000-11997600	Weak transcription	Right Atrium	heart
26	chr18:11996000-11998000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr18:11996000-11998000	Weak transcription	Fetal Lung	lung
28	chr18:11996000-11998000	Weak transcription	NHDF-Ad	bronchial
29	chr18:11996000-11998200	Weak transcription	Brain Angular Gyrus	brain
30	chr18:11996000-11998600	Weak transcription	HSMM	muscle
31	chr18:11996000-11999200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr18:11996000-11999200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr18:11996000-11999200	Weak transcription	Fetal Intestine Large	intestine
34	chr18:11996000-11999200	Enhancers	HepG2	liver
35	chr18:11996000-12001400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr18:11996000-12001400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr18:11996000-12004000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr18:11996000-12004800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr18:11996000-12004800	Weak transcription	HMEC	breast
40	chr18:11996000-12005600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr18:11996200-11998000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr18:11996200-11998400	Weak transcription	Fetal Kidney	kidney
43	chr18:11996200-11998400	Enhancers	Lung	lung
44	chr18:11996200-11999000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr18:11996200-11999000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr18:11996200-11999000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr18:11996200-11999000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr18:11996200-11999000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr18:11996200-11999200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr18:11996200-11999200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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