Variant report

Variant	rs2884174
Chromosome Location	chr2:10020659-10020660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10015734..10018207-chr2:10020455..10022125,2	K562	blood:
2	chr2:10016707..10019550-chr2:10020625..10023178,3	K562	blood:
3	chr2:10019152..10020684-chr2:10028239..10030255,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1119632	0.81[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1119633	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11887231	0.88[ASN][1000 genomes]
rs13404815	0.83[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs13429581	0.88[ASN][1000 genomes]
rs16867192	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16867203	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656329	0.83[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs287975	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287976	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287977	0.83[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs287978	0.88[ASN][1000 genomes]
rs287979	0.82[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs287980	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287981	0.84[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs287982	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs56154233	0.88[ASN][1000 genomes]
rs57352580	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58521916	0.88[ASN][1000 genomes]
rs72780999	0.95[ASN][1000 genomes]
rs72782605	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72782633	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72782634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782637	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973577	0.88[ASN][1000 genomes]
rs9973654	0.88[ASN][1000 genomes]
rs9973905	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv873630	chr2:9953949-10030024	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
4	nsv873631	chr2:9975557-10059770	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
5	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv580960	chr2:9993451-10066694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
8	nsv873632	chr2:10000978-10045014	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2884174	TAF1B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9987200-10038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:9993800-10079600	Weak transcription	Gastric	stomach
3	chr2:9995800-10038000	Weak transcription	Small Intestine	intestine
4	chr2:9998200-10024000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:9998200-10035600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:9998600-10024000	Weak transcription	Pancreas	Pancrea
7	chr2:9998800-10026000	Weak transcription	Fetal Brain Male	brain
8	chr2:9998800-10032200	Weak transcription	Fetal Heart	heart
9	chr2:9998800-10036400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:9999000-10024000	Weak transcription	Colonic Mucosa	Colon
11	chr2:9999000-10024000	Weak transcription	Spleen	Spleen
12	chr2:9999000-10035800	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:9999000-10035800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:9999000-10037000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:9999000-10037200	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:9999200-10036200	Weak transcription	Brain Angular Gyrus	brain
17	chr2:9999200-10036400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:9999200-10053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:10001600-10024000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:10001600-10024000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:10002200-10024200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:10007800-10021000	Strong transcription	A549	lung
23	chr2:10007800-10026200	Strong transcription	Dnd41	blood
24	chr2:10008000-10026800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:10008200-10028000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr2:10008400-10026600	Weak transcription	GM12878-XiMat	blood
27	chr2:10008600-10020800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:10008600-10021000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:10008800-10021000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:10009000-10024000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:10009600-10020800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:10010200-10021000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:10010200-10021200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:10010800-10021000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:10011600-10022200	Strong transcription	Fetal Thymus	thymus
36	chr2:10011800-10020800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:10012000-10021400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:10013000-10020800	Strong transcription	Primary B cells from cord blood	blood
39	chr2:10013200-10020800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:10013600-10020800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:10013800-10021000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:10014000-10021000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr2:10014200-10020800	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:10014600-10020800	Strong transcription	Fetal Lung	lung
45	chr2:10014600-10020800	Strong transcription	Lung	lung
46	chr2:10014600-10020800	Strong transcription	Thymus	Thymus
47	chr2:10014600-10024000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:10014800-10045400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr2:10015000-10036200	Weak transcription	Fetal Kidney	kidney
50	chr2:10015200-10024000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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