Variant report

Variant	rs12678639
Chromosome Location	chr8:52830648-52830649
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:52829314..52832540-chr8:52837482..52840853,3	MCF-7	breast:
2	chr8:52805769..52807852-chr8:52829982..52831836,2	K562	blood:
3	chr8:52813732..52817292-chr8:52828515..52831149,4	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10087958	0.82[JPT][hapmap]
rs10504130	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10958300	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958301	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11775587	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11775611	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11777016	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11777714	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778849	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11780040	0.96[ASN][1000 genomes]
rs11780891	0.81[AMR][1000 genomes]
rs11781330	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11784869	1.00[ASN][1000 genomes]
rs11785805	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11786167	0.81[AMR][1000 genomes]
rs11787229	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12675786	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12675907	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12676345	0.84[ASN][1000 genomes]
rs12676780	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12676835	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12677407	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12679287	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12679983	0.83[ASN][1000 genomes]
rs12680128	0.83[ASN][1000 genomes]
rs12681203	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12681734	0.91[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs13265006	0.96[ASN][1000 genomes]
rs13276400	0.84[ASN][1000 genomes]
rs16916820	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16916856	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16916865	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16916906	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16916961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17212214	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17212256	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17284746	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2037138	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2037139	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069119	0.84[ASN][1000 genomes]
rs2176120	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34058697	0.94[ASN][1000 genomes]
rs34073804	0.85[ASN][1000 genomes]
rs34213209	0.84[ASN][1000 genomes]
rs34319820	0.85[ASN][1000 genomes]
rs34364864	0.94[ASN][1000 genomes]
rs34372756	1.00[ASN][1000 genomes]
rs34677273	1.00[ASN][1000 genomes]
rs34973406	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35032384	1.00[ASN][1000 genomes]
rs35509250	0.84[ASN][1000 genomes]
rs35603537	0.84[ASN][1000 genomes]
rs41453644	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4292674	0.83[ASN][1000 genomes]
rs4321994	0.82[ASN][1000 genomes]
rs4534123	0.83[ASN][1000 genomes]
rs4598243	0.91[ASN][1000 genomes]
rs4626585	0.83[ASN][1000 genomes]
rs57212480	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58561048	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58583070	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59602923	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60153173	0.85[ASN][1000 genomes]
rs60304457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60796336	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61326367	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6768	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6994203	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs71513549	0.83[ASN][1000 genomes]
rs71513552	0.85[ASN][1000 genomes]
rs71513561	0.96[ASN][1000 genomes]
rs71513564	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs763550	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9650179	1.00[ASN][1000 genomes]
rs9650180	1.00[ASN][1000 genomes]
rs9650305	1.00[ASN][1000 genomes]
rs9792352	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12678639	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52812800-52833400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:52813200-52831000	Weak transcription	Right Ventricle	heart
3	chr8:52813200-52833200	Weak transcription	Brain Angular Gyrus	brain
4	chr8:52813400-52837200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr8:52813600-52837400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:52813800-52831600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:52813800-52831600	Weak transcription	Fetal Stomach	stomach
8	chr8:52813800-52833200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:52813800-52835800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr8:52813800-52837400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr8:52814000-52833200	Weak transcription	Fetal Lung	lung
12	chr8:52814000-52833600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr8:52814000-52836200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:52814000-52837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:52814000-52839200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr8:52814200-52842000	Weak transcription	Brain Substantia Nigra	brain
17	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
18	chr8:52814800-52834200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr8:52814800-52834600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr8:52814800-52837200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
22	chr8:52815200-52833000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr8:52815200-52837400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr8:52816200-52831000	Weak transcription	Primary T cells from cord blood	blood
25	chr8:52817200-52830800	Weak transcription	Left Ventricle	heart
26	chr8:52817200-52830800	Weak transcription	Ovary	ovary
27	chr8:52817200-52833400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr8:52817800-52831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr8:52818000-52834800	Weak transcription	Pancreas	Pancrea
30	chr8:52819400-52834200	Weak transcription	Psoas Muscle	Psoas
31	chr8:52822400-52837800	Weak transcription	Esophagus	oesophagus
32	chr8:52822600-52860200	Weak transcription	Fetal Muscle Leg	muscle
33	chr8:52823000-52830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr8:52823000-52833600	Weak transcription	Thymus	Thymus
35	chr8:52823000-52834800	Weak transcription	Fetal Intestine Small	intestine
36	chr8:52823000-52840200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr8:52823600-52838200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr8:52824200-52831600	Weak transcription	Aorta	Aorta
39	chr8:52824800-52832600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr8:52826800-52834800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr8:52827200-52833600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr8:52827400-52830800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr8:52827600-52836600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr8:52827800-52835800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr8:52828000-52831000	Weak transcription	Adipose Nuclei	Adipose
46	chr8:52828000-52831000	Weak transcription	Fetal Intestine Large	intestine
47	chr8:52828000-52831000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr8:52828200-52830800	Weak transcription	Primary B cells from cord blood	blood
49	chr8:52828200-52830800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr8:52828200-52832600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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