Variant report

Variant	rs16916906
Chromosome Location	chr8:52781693-52781694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:52781440..52784633-chr8:52809413..52813139,4	MCF-7	breast:
2	chr8:52780733..52786342-chr8:52810229..52813272,6	MCF-7	breast:
3	chr8:52778955..52782186-chr8:52783588..52785902,4	K562	blood:

Variant related genes	Relation type
ENSG00000228801	Chromatin interaction
ENSG00000168300	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10504130	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958305	0.96[ASN][1000 genomes]
rs11775587	0.96[ASN][1000 genomes]
rs11775611	0.96[ASN][1000 genomes]
rs11777016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778849	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11780040	1.00[ASN][1000 genomes]
rs11780891	0.90[AMR][1000 genomes]
rs11781330	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11784869	0.96[ASN][1000 genomes]
rs11785805	0.96[ASN][1000 genomes]
rs11786167	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11787229	0.88[ASN][1000 genomes]
rs12675786	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12675907	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12676345	0.87[ASN][1000 genomes]
rs12676780	0.95[ASN][1000 genomes]
rs12676835	0.96[ASN][1000 genomes]
rs12677407	0.96[ASN][1000 genomes]
rs12678639	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12678680	0.83[AMR][1000 genomes]
rs12679287	0.96[ASN][1000 genomes]
rs12679983	0.86[ASN][1000 genomes]
rs12680128	0.86[ASN][1000 genomes]
rs12681203	0.96[ASN][1000 genomes]
rs12681734	1.00[ASN][1000 genomes]
rs13265006	1.00[ASN][1000 genomes]
rs13276400	0.87[ASN][1000 genomes]
rs16916820	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16916856	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16916865	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16916961	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17212214	0.96[ASN][1000 genomes]
rs17212256	0.96[ASN][1000 genomes]
rs17284746	0.96[ASN][1000 genomes]
rs2037138	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037139	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069119	0.87[ASN][1000 genomes]
rs2176120	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34058697	0.98[ASN][1000 genomes]
rs34073804	0.88[ASN][1000 genomes]
rs34213209	0.87[ASN][1000 genomes]
rs34319820	0.88[ASN][1000 genomes]
rs34364864	0.98[ASN][1000 genomes]
rs34372756	0.96[ASN][1000 genomes]
rs34677273	0.96[ASN][1000 genomes]
rs34973406	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35032384	0.96[ASN][1000 genomes]
rs35509250	0.87[ASN][1000 genomes]
rs35603537	0.87[ASN][1000 genomes]
rs41453644	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4292674	0.86[ASN][1000 genomes]
rs4321994	0.85[ASN][1000 genomes]
rs4534123	0.86[ASN][1000 genomes]
rs4598243	0.94[ASN][1000 genomes]
rs4626585	0.86[ASN][1000 genomes]
rs57212480	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58561048	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58583070	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59602923	0.96[ASN][1000 genomes]
rs60153173	0.88[ASN][1000 genomes]
rs60304457	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60796336	0.96[ASN][1000 genomes]
rs61326367	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6994203	0.93[ASN][1000 genomes]
rs71513549	0.86[ASN][1000 genomes]
rs71513552	0.88[ASN][1000 genomes]
rs71513561	1.00[ASN][1000 genomes]
rs71513564	0.96[ASN][1000 genomes]
rs763550	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9650179	0.96[ASN][1000 genomes]
rs9650180	0.96[ASN][1000 genomes]
rs9650305	0.96[ASN][1000 genomes]
rs9792352	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv526922	chr8:52772515-52786791	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16916906	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52733200-52783800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:52739800-52782600	Weak transcription	K562	blood
3	chr8:52759000-52786200	Weak transcription	Lung	lung
4	chr8:52759200-52786200	Weak transcription	Spleen	Spleen
5	chr8:52763800-52781800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr8:52764000-52781800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr8:52764000-52783600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr8:52764000-52793400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr8:52764200-52782400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr8:52767400-52796600	Weak transcription	Fetal Brain Male	brain
11	chr8:52769800-52782600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:52769800-52785200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:52769800-52793600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr8:52771000-52797800	Weak transcription	Fetal Stomach	stomach
15	chr8:52771800-52782600	Weak transcription	NHLF	lung
16	chr8:52771800-52786200	Weak transcription	Gastric	stomach
17	chr8:52771800-52797000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr8:52771800-52810800	Weak transcription	Esophagus	oesophagus
19	chr8:52772000-52781800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr8:52772000-52783800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr8:52772000-52783800	Weak transcription	Ovary	ovary
22	chr8:52772200-52782600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr8:52772200-52807600	Weak transcription	HSMMtube	muscle
24	chr8:52772400-52782600	Weak transcription	HSMM	muscle
25	chr8:52772400-52793200	Weak transcription	Fetal Heart	heart
26	chr8:52772600-52782600	Weak transcription	NH-A	brain
27	chr8:52772600-52786000	Weak transcription	Pancreas	Pancrea
28	chr8:52772800-52781800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr8:52772800-52782600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr8:52772800-52782600	Weak transcription	HUVEC	blood vessel
31	chr8:52773000-52781800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr8:52773000-52786000	Weak transcription	Psoas Muscle	Psoas
33	chr8:52773000-52791200	Weak transcription	Thymus	Thymus
34	chr8:52773000-52803200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr8:52773200-52781800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr8:52773200-52782600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr8:52773200-52782600	Weak transcription	NHEK	skin
38	chr8:52773600-52782400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr8:52773600-52797000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr8:52773600-52797200	Weak transcription	Placenta	Placenta
41	chr8:52775600-52782400	Weak transcription	Brain Anterior Caudate	brain
42	chr8:52775600-52786200	Weak transcription	Small Intestine	intestine
43	chr8:52776600-52782400	Weak transcription	Left Ventricle	heart
44	chr8:52776600-52782800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr8:52778000-52781800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr8:52779000-52781800	Weak transcription	Fetal Muscle Leg	muscle
47	chr8:52779200-52781800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr8:52779400-52781800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr8:52779400-52781800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr8:52779400-52782200	Weak transcription	Adipose Nuclei	Adipose

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