Variant report

Variant	rs627965
Chromosome Location	chr18:12035994-12035995
allele	G/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	chr18:12034235-12036794	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr18:12035769-12036071	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12035639..12037274-chr18:12041657..12044195,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267480	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1662608	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1787982	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2165855	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2849394	0.86[ASN][1000 genomes]
rs2849395	0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2849396	0.86[ASN][1000 genomes]
rs2849397	0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2849398	0.86[ASN][1000 genomes]
rs2849399	0.86[ASN][1000 genomes]
rs2851911	0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2851912	0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2851914	0.88[ASN][1000 genomes]
rs2851918	0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs4291976	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4580259	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4580260	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4797608	0.90[ASN][1000 genomes]
rs4797609	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs4797610	0.90[ASN][1000 genomes]
rs4797611	0.90[ASN][1000 genomes]
rs582959	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs591447	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622443	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs630110	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs639876	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs639966	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs640340	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs642585	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6505709	0.86[ASN][1000 genomes]
rs655651	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657476	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8090265	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
11	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
12	nsv909393	chr18:12001258-12155371	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv909394	chr18:12017343-12141372	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs627965	MC5R	cis	parietal	SCAN
rs627965	PSMG2	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12016200-12038000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr18:12017600-12038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr18:12024200-12038400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr18:12027400-12038400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:12028800-12038200	Weak transcription	Psoas Muscle	Psoas
6	chr18:12028800-12038400	Weak transcription	Right Atrium	heart
7	chr18:12029000-12036000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr18:12029000-12037400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr18:12029000-12038000	Weak transcription	HMEC	breast
10	chr18:12029000-12038200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr18:12030200-12038200	Weak transcription	Ovary	ovary
12	chr18:12030600-12038000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr18:12030600-12038400	Weak transcription	Lung	lung
14	chr18:12030800-12038000	Weak transcription	A549	lung
15	chr18:12031200-12038000	Weak transcription	Colonic Mucosa	Colon
16	chr18:12031200-12038200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr18:12031400-12038000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr18:12031400-12038000	Weak transcription	Fetal Intestine Large	intestine
19	chr18:12031400-12038200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr18:12031400-12038200	Weak transcription	Stomach Mucosa	stomach
21	chr18:12031400-12038200	Weak transcription	Spleen	Spleen
22	chr18:12031400-12038800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr18:12031800-12038400	Weak transcription	Aorta	Aorta
24	chr18:12032000-12037800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr18:12032000-12038200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr18:12032200-12036400	Weak transcription	NHEK	skin
27	chr18:12032200-12038200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr18:12032400-12036400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr18:12032400-12038000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:12032400-12038400	Weak transcription	Fetal Lung	lung
31	chr18:12032600-12038000	Weak transcription	Colon Smooth Muscle	Colon
32	chr18:12032600-12038400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr18:12033200-12036200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr18:12033200-12038200	Weak transcription	Adipose Nuclei	Adipose
35	chr18:12033400-12036400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr18:12033400-12037200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr18:12033600-12036400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:12033600-12037400	Weak transcription	Fetal Intestine Small	intestine
39	chr18:12033600-12038200	Weak transcription	Gastric	stomach
40	chr18:12033600-12038200	Weak transcription	Left Ventricle	heart
41	chr18:12033600-12038400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr18:12033800-12038000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr18:12033800-12038200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr18:12033800-12038600	Weak transcription	Hela-S3	cervix
45	chr18:12034000-12038000	Weak transcription	Fetal Muscle Leg	muscle
46	chr18:12034000-12038000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr18:12034000-12038000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr18:12034000-12038400	Weak transcription	NHDF-Ad	bronchial
49	chr18:12034200-12038000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr18:12034400-12038200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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