Variant report

Variant	rs630110
Chromosome Location	chr18:12029857-12029858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12025555..12027976-chr18:12028619..12030454,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1662608	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1787982	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165855	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2849394	0.88[ASN][1000 genomes]
rs2849395	0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2849396	0.88[ASN][1000 genomes]
rs2849397	0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2849398	0.88[ASN][1000 genomes]
rs2849399	0.88[ASN][1000 genomes]
rs2851911	0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2851912	0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2851913	0.81[ASN][1000 genomes]
rs2851914	0.90[ASN][1000 genomes]
rs2851918	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4291976	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4580259	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4580260	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4797608	0.92[ASN][1000 genomes]
rs4797609	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4797610	0.92[ASN][1000 genomes]
rs4797611	0.92[ASN][1000 genomes]
rs582959	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs591447	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs622443	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs627965	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	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639966	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640340	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs642585	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6505709	0.88[ASN][1000 genomes]
rs655651	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs657476	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8090265	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
13	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
14	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
rs630110	MC5R	cis	parietal	SCAN
rs630110	PSMG2	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11996600-12035000	Weak transcription	Primary T cells from cord blood	blood
2	chr18:11996800-12034400	Weak transcription	Primary B cells from cord blood	blood
3	chr18:11997000-12034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr18:11998400-12034000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr18:11999000-12034000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr18:11999000-12035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr18:11999200-12035800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr18:12015800-12030400	Strong transcription	Fetal Stomach	stomach
9	chr18:12016000-12032400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr18:12016000-12032400	Weak transcription	HSMM	muscle
11	chr18:12016200-12038000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr18:12016400-12030200	Weak transcription	Fetal Kidney	kidney
13	chr18:12016400-12032600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr18:12016600-12032400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr18:12017600-12031800	Weak transcription	Osteobl	bone
16	chr18:12017600-12038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr18:12023000-12033400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr18:12023200-12033600	Strong transcription	Fetal Intestine Small	intestine
19	chr18:12023400-12033000	Weak transcription	HSMMtube	muscle
20	chr18:12023800-12031400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr18:12024200-12038400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr18:12025600-12030000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr18:12026800-12031400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr18:12027000-12032000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr18:12027200-12033400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr18:12027400-12030400	Weak transcription	Left Ventricle	heart
27	chr18:12027400-12031200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr18:12027400-12032000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr18:12027400-12033800	Strong transcription	Hela-S3	cervix
30	chr18:12027400-12038400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:12027800-12031200	Strong transcription	Gastric	stomach
32	chr18:12027800-12031400	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr18:12027800-12032400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr18:12027800-12032400	Strong transcription	Placenta	Placenta
35	chr18:12028000-12030000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
36	chr18:12028000-12030400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr18:12028000-12031200	Strong transcription	Colonic Mucosa	Colon
38	chr18:12028000-12031800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr18:12028000-12032800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr18:12028000-12033000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr18:12028000-12033400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr18:12028000-12034400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr18:12028200-12030400	Strong transcription	Right Ventricle	heart
44	chr18:12028200-12031200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr18:12028200-12031400	Strong transcription	Fetal Intestine Large	intestine
46	chr18:12028200-12031400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr18:12028200-12031400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr18:12028200-12032200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr18:12028200-12032200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr18:12028200-12032600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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