Variant report

Variant	rs2542174
Chromosome Location	chr18:12700689-12700690
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12677577..12680065-chr18:12699898..12703044,3	K562	blood:
2	chr18:12699667..12702594-chr18:12881299..12884281,3	K562	blood:
3	chr18:12689483..12696263-chr18:12698961..12704404,9	MCF-7	breast:
4	chr18:12700182..12704223-chr18:12944670..12949511,9	K562	blood:
5	chr18:12406252..12409116-chr18:12699672..12701773,2	MCF-7	breast:
6	chr18:12685127..12688617-chr18:12697968..12702228,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction
ENSG00000141391	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11663219	0.84[ASN][1000 genomes]
rs11663226	0.83[ASN][1000 genomes]
rs11663260	0.84[ASN][1000 genomes]
rs1539813	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16939680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1833326	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1893212	0.92[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1893213	0.82[JPT][hapmap]
rs1893214	0.82[ASN][1000 genomes]
rs2015197	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2542172	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542176	0.84[ASN][1000 genomes]
rs2847254	0.84[ASN][1000 genomes]
rs2847272	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2847305	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4796966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4797698	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4797701	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs479860	0.92[CHB][hapmap]
rs507868	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs514831	0.92[CHB][hapmap]
rs56063272	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56328751	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs575093	0.93[CHB][hapmap]
rs58135011	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60876158	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61542301	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61635631	0.82[AMR][1000 genomes]
rs62095972	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62097130	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62097132	0.84[AMR][1000 genomes]
rs62097145	0.82[ASN][1000 genomes]
rs8086774	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap]
rs8089003	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9635805	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
11	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12658800-12701800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:12660400-12700800	Weak transcription	Fetal Brain Male	brain
3	chr18:12662800-12701600	Weak transcription	Aorta	Aorta
4	chr18:12667000-12701600	Weak transcription	Gastric	stomach
5	chr18:12672200-12701400	Weak transcription	Colonic Mucosa	Colon
6	chr18:12673200-12701600	Weak transcription	Psoas Muscle	Psoas
7	chr18:12674600-12701600	Weak transcription	Right Ventricle	heart
8	chr18:12674600-12701600	Weak transcription	Small Intestine	intestine
9	chr18:12674800-12701400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr18:12678200-12701400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr18:12678400-12701200	Weak transcription	NH-A	brain
12	chr18:12678400-12701600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:12678400-12701600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr18:12678400-12701600	Weak transcription	HSMMtube	muscle
15	chr18:12679600-12701000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr18:12679600-12701000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr18:12679600-12701200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr18:12679600-12701600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr18:12679800-12701000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr18:12679800-12701000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr18:12679800-12701000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr18:12680000-12701200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr18:12680000-12701600	Weak transcription	Esophagus	oesophagus
24	chr18:12680000-12701600	Weak transcription	Ovary	ovary
25	chr18:12680200-12700800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr18:12680800-12701400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr18:12684800-12701600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr18:12685200-12701600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr18:12685400-12701400	Weak transcription	Fetal Intestine Small	intestine
30	chr18:12685600-12701400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr18:12686400-12701000	Weak transcription	Brain Hippocampus Middle	brain
32	chr18:12686800-12700800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr18:12686800-12701600	Weak transcription	Lung	lung
34	chr18:12687200-12701000	Weak transcription	Primary B cells from cord blood	blood
35	chr18:12687200-12701200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr18:12687400-12701000	Weak transcription	Fetal Lung	lung
37	chr18:12688400-12701400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:12690600-12701000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr18:12691000-12700800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr18:12692600-12700800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr18:12692600-12701400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr18:12693000-12701000	Weak transcription	Brain Germinal Matrix	brain
43	chr18:12693800-12701000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr18:12694200-12701000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr18:12694200-12701200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr18:12694200-12701600	Weak transcription	Fetal Stomach	stomach
47	chr18:12694400-12701200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr18:12694600-12701600	Weak transcription	Left Ventricle	heart
49	chr18:12694600-12701600	Weak transcription	Pancreas	Pancrea
50	chr18:12694600-12701600	Weak transcription	Stomach Mucosa	stomach

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