Variant report

Variant	rs2288644
Chromosome Location	chr2:10079170-10079171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10077387..10079466-chr2:10182113..10184414,2	MCF-7	breast:
2	chr2:9982989..9985362-chr2:10078538..10080122,2	MCF-7	breast:
3	chr2:10077034..10079332-chr2:10081722..10084624,2	MCF-7	breast:
4	chr2:10078268..10079788-chr2:10084241..10085937,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAF1B-2	chr2:10076489-10079719	ENSG00000269973.1

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction
ENSG00000115750	Chromatin interaction
ENSG00000172059	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1014509	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs1036056	0.90[CHB][hapmap]
rs1036057	0.83[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1036058	0.84[ASN][1000 genomes]
rs10495575	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1062160	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10929617	0.82[ASN][1000 genomes]
rs10929618	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1132838	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12468582	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12470216	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12476490	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12478489	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12611655	0.82[ASN][1000 genomes]
rs12613533	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12613568	0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12617615	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12619769	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12622420	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12623017	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs12623213	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12623372	0.95[ASN][1000 genomes]
rs1367386	0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1469542	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs1469543	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1469544	0.93[CEU][hapmap];0.88[CHB][hapmap]
rs1469545	0.95[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap]
rs1473962	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs16867195	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs16867196	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs16867211	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs16867215	0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs16867242	0.87[ASN][1000 genomes]
rs1835427	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2280150	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2280151	0.86[ASN][1000 genomes]
rs2288640	0.99[ASN][1000 genomes]
rs4143791	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs452480	0.90[CEU][hapmap]
rs4610025	0.80[ASN][1000 genomes]
rs4669470	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs4669471	0.94[CEU][hapmap]
rs4669475	0.80[ASN][1000 genomes]
rs4669476	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs4669477	0.82[ASN][1000 genomes]
rs4669478	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4669479	0.83[ASN][1000 genomes]
rs4669481	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs4669484	0.95[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs4669485	0.86[ASN][1000 genomes]
rs4669486	0.86[ASN][1000 genomes]
rs4669488	0.86[ASN][1000 genomes]
rs4669501	0.96[ASN][1000 genomes]
rs4669506	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62127130	0.80[ASN][1000 genomes]
rs62127133	0.80[ASN][1000 genomes]
rs62127134	0.80[ASN][1000 genomes]
rs62127136	0.80[ASN][1000 genomes]
rs62127138	0.82[ASN][1000 genomes]
rs62127140	0.83[ASN][1000 genomes]
rs62127143	0.83[ASN][1000 genomes]
rs62127144	0.83[ASN][1000 genomes]
rs62127145	0.85[ASN][1000 genomes]
rs62127146	0.85[ASN][1000 genomes]
rs62127463	0.87[ASN][1000 genomes]
rs62127466	0.88[ASN][1000 genomes]
rs62127471	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718255	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs718256	0.86[ASN][1000 genomes]
rs72782635	0.82[ASN][1000 genomes]
rs7579559	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs7602449	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7608055	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]

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	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
2	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
3	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
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2288644	TAF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:10038600-10079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:10045800-10079600	Weak transcription	Esophagus	oesophagus
7	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
8	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:10055000-10080800	Weak transcription	Pancreas	Pancrea
11	chr2:10055000-10080800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:10055200-10079600	Weak transcription	K562	blood
14	chr2:10055200-10080800	Weak transcription	HMEC	breast
15	chr2:10059000-10080600	Weak transcription	HSMMtube	muscle
16	chr2:10059400-10081200	Weak transcription	GM12878-XiMat	blood
17	chr2:10060600-10080200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:10061000-10079600	Weak transcription	HepG2	liver
19	chr2:10061000-10080800	Weak transcription	Brain Germinal Matrix	brain
20	chr2:10061000-10080800	Weak transcription	NH-A	brain
21	chr2:10061000-10080800	Weak transcription	NHEK	skin
22	chr2:10062600-10080200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:10063000-10080800	Weak transcription	NHLF	lung
24	chr2:10064200-10079400	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:10064200-10080200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:10064600-10079200	Weak transcription	Fetal Brain Female	brain
27	chr2:10065000-10080800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:10069600-10079800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:10070800-10080800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:10073400-10081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:10073400-10084400	Weak transcription	Lung	lung
32	chr2:10073600-10088800	Weak transcription	Spleen	Spleen
33	chr2:10073800-10080000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:10073800-10080800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:10073800-10080800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:10073800-10081000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:10073800-10082000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:10074000-10079200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:10074000-10079200	Weak transcription	HUVEC	blood vessel
40	chr2:10074000-10079400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:10074000-10079600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:10074000-10079600	Weak transcription	Fetal Intestine Large	intestine
43	chr2:10074000-10079800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:10074000-10081800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr2:10074200-10081800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:10074400-10079400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:10074400-10080200	Weak transcription	HSMM	muscle
48	chr2:10074400-10080800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:10074800-10079800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:10074800-10080000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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