Variant report

Variant	rs2176120
Chromosome Location	chr8:52798022-52798023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:52789836..52792146-chr8:52797472..52799368,2	K562	blood:
2	chr8:52796441..52798988-chr8:52800960..52803935,3	K562	blood:
3	chr8:52796166..52799538-chr8:52799577..52802890,4	MCF-7	breast:
4	chr8:52795079..52798065-chr8:52810619..52812856,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168300	Chromatin interaction
ENSG00000228801	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10504130	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958300	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958301	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[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	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777714	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778849	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11780040	1.00[ASN][1000 genomes]
rs11780891	0.85[AMR][1000 genomes]
rs11781330	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[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];0.85[AMR][1000 genomes]
rs11787229	0.88[ASN][1000 genomes]
rs12675786	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12675907	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12676345	0.87[ASN][1000 genomes]
rs12676780	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12676835	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12677407	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12678639	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12679287	0.96[ASN][1000 genomes]
rs12679983	0.86[ASN][1000 genomes]
rs12680128	0.86[ASN][1000 genomes]
rs12681203	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12681734	1.00[ASN][1000 genomes]
rs13265006	1.00[ASN][1000 genomes]
rs13276400	0.87[ASN][1000 genomes]
rs16916820	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16916856	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16916865	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16916906	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16916961	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17212214	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17212256	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17284746	0.96[ASN][1000 genomes]
rs2037138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069119	0.87[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];0.92[AMR][1000 genomes];0.96[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];0.90[AMR][1000 genomes];0.94[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	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58561048	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58583070	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59602923	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60153173	0.88[ASN][1000 genomes]
rs60304457	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60796336	0.96[ASN][1000 genomes]
rs61326367	0.88[AMR][1000 genomes];0.86[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	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs763550	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs2176120	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52771800-52810800	Weak transcription	Esophagus	oesophagus
2	chr8:52772200-52807600	Weak transcription	HSMMtube	muscle
3	chr8:52773000-52803200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr8:52779400-52809000	Weak transcription	Fetal Kidney	kidney
5	chr8:52780800-52803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr8:52782200-52809600	Weak transcription	Aorta	Aorta
7	chr8:52783000-52803200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr8:52783000-52803400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:52783000-52803600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:52784000-52806600	Weak transcription	Hela-S3	cervix
11	chr8:52784200-52806600	Weak transcription	A549	lung
12	chr8:52789200-52799600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr8:52795200-52799400	Weak transcription	Ovary	ovary
14	chr8:52795600-52798400	Enhancers	Brain Hippocampus Middle	brain
15	chr8:52795600-52800200	Enhancers	Primary T cells from cord blood	blood
16	chr8:52795800-52798200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:52795800-52798800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr8:52796000-52799800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr8:52796200-52798200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr8:52796200-52798200	Enhancers	Brain Substantia Nigra	brain
21	chr8:52796200-52798200	Enhancers	Rectal Smooth Muscle	rectum
22	chr8:52796200-52798400	Enhancers	Adipose Nuclei	Adipose
23	chr8:52796200-52798400	Enhancers	Brain Cingulate Gyrus	brain
24	chr8:52796200-52798400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr8:52796200-52798600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr8:52796200-52798600	Enhancers	Brain Germinal Matrix	brain
27	chr8:52796200-52798800	Enhancers	Small Intestine	intestine
28	chr8:52796200-52800000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr8:52796200-52800200	Enhancers	Colon Smooth Muscle	Colon
30	chr8:52796400-52798200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr8:52796400-52798400	Enhancers	Brain Angular Gyrus	brain
32	chr8:52796400-52798400	Enhancers	Duodenum Mucosa	Duodenum
33	chr8:52796400-52800000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr8:52796600-52798800	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr8:52796600-52799400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr8:52796600-52799800	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr8:52796600-52799800	Enhancers	Fetal Heart	heart
38	chr8:52796600-52800000	Enhancers	Primary hematopoietic stem cells	blood
39	chr8:52796600-52800200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr8:52796800-52798200	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr8:52796800-52798800	Enhancers	Primary B cells from peripheral blood	blood
42	chr8:52796800-52798800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr8:52796800-52798800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr8:52796800-52799000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr8:52796800-52799800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr8:52796800-52799800	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr8:52796800-52800000	Enhancers	Fetal Thymus	thymus
48	chr8:52796800-52800000	Enhancers	Thymus	Thymus
49	chr8:52796800-52800200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr8:52797000-52798200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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