Variant report

Variant	rs287988
Chromosome Location	chr2:9987958-9987959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9977777..9980395-chr2:9987504..9989873,2	MCF-7	breast:
2	chr2:9983867..9985746-chr2:9987128..9988771,2	K562	blood:
3	chr2:9981927..9985713-chr2:9987570..9993259,7	MCF-7	breast:
4	chr2:9985747..9988019-chr2:10062440..10064881,2	MCF-7	breast:
5	chr2:9986181..9988070-chr2:9991011..9993550,2	MCF-7	breast:
6	chr2:9972444..9974015-chr2:9987549..9989213,2	MCF-7	breast:
7	chr2:9981404..9986079-chr2:9986481..9992681,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11692193	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008782	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs287972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287974	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs287986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287987	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287993	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287994	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287995	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287996	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287999	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs388570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447465	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs451412	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs514805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572907	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6731044	1.00[ASN][1000 genomes]
rs7599798	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv873629	chr2:9949464-10016627	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs287988	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx
rs287988	TAF1B	cis	Nerve Tibial	GTEx
rs287988	TAF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9984200-9994000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:9984600-9990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:9984600-9992600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:9984600-9995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:9984800-9997600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:9984800-9998400	Weak transcription	Pancreas	Pancrea
7	chr2:9985000-9990400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:9985000-9990800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:9985000-9991000	Weak transcription	Colonic Mucosa	Colon
10	chr2:9985000-9992000	Weak transcription	Brain Substantia Nigra	brain
11	chr2:9985000-9992000	Weak transcription	Lung	lung
12	chr2:9985000-9992000	Weak transcription	Ovary	ovary
13	chr2:9985000-9992200	Weak transcription	Fetal Stomach	stomach
14	chr2:9985000-9992200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:9985000-9993600	Weak transcription	Right Ventricle	heart
16	chr2:9985000-10000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:9985200-9989600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:9985200-9995600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:9985200-9997200	Weak transcription	Fetal Heart	heart
20	chr2:9985400-9988200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:9985400-9988400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:9985400-9989800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:9985400-9993800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:9985400-9995400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:9985400-9995400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:9985400-9995400	Weak transcription	Small Intestine	intestine
27	chr2:9985600-9988200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:9985600-9988200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:9985600-9989200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:9985600-9989600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:9985600-9989800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:9985600-9990600	Weak transcription	HSMMtube	muscle
33	chr2:9985600-9993800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:9985600-9995400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:9985600-9997200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:9985800-9997000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:9986200-9988000	Strong transcription	Primary B cells from cord blood	blood
38	chr2:9986200-9988000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:9986200-9988000	Strong transcription	Liver	Liver
40	chr2:9986200-9988800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr2:9986200-9997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:9986400-9993000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:9986600-9992200	Weak transcription	Fetal Intestine Small	intestine
44	chr2:9986600-9996200	Strong transcription	A549	lung
45	chr2:9986800-9988000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:9986800-9990000	Weak transcription	Fetal Kidney	kidney
47	chr2:9986800-9990400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr2:9986800-9992400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:9987000-9989400	Weak transcription	GM12878-XiMat	blood
50	chr2:9987000-9990400	Weak transcription	Rectal Smooth Muscle	rectum

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