Variant report

Variant	rs287986
Chromosome Location	chr2:9985606-9985607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9983066..9987186-chr2:10091615..10095343,4	MCF-7	breast:
2	chr2:9984016..9986818-chr2:10112280..10114129,2	MCF-7	breast:
3	chr2:9983867..9985746-chr2:9987128..9988771,2	K562	blood:
4	chr2:9984123..9986772-chr2:10086772..10088957,2	K562	blood:
5	chr2:9982271..9986804-chr2:10090021..10093067,7	K562	blood:
6	chr2:9983691..9985832-chr2:10083772..10085914,3	MCF-7	breast:
7	chr2:9936512..9939080-chr2:9983882..9985731,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11692193	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477755	0.80[AFR][1000 genomes]
rs13008782	0.84[ASN][1000 genomes]
rs1709854	0.80[AFR][1000 genomes]
rs17364189	0.85[YRI][hapmap]
rs2241664	0.80[AFR][1000 genomes]
rs287972	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287974	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs287987	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287992	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287993	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287996	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287997	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287999	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35029226	0.80[AFR][1000 genomes]
rs369551	0.80[AFR][1000 genomes]
rs369605	0.82[YRI][hapmap]
rs371305	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs372031	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs374197	0.80[AFR][1000 genomes]
rs375793	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs382747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs386355	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs388570	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs388695	0.80[AFR][1000 genomes]
rs389002	0.80[AFR][1000 genomes]
rs391889	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs396281	0.80[AFR][1000 genomes]
rs397498	0.80[AFR][1000 genomes]
rs397871	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs400758	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs403317	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs407874	0.80[AFR][1000 genomes]
rs410121	0.80[AFR][1000 genomes]
rs411413	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs412039	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs414499	0.80[AFR][1000 genomes]
rs415676	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs416228	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs420122	0.80[AFR][1000 genomes]
rs423651	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs431519	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs431562	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs437662	0.80[AFR][1000 genomes]
rs437906	0.80[AFR][1000 genomes]
rs438762	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs438966	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs439310	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs444650	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs447465	0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs447476	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs448287	0.85[YRI][hapmap]
rs449472	0.85[YRI][hapmap]
rs450286	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs450643	0.80[AFR][1000 genomes]
rs451045	0.80[AFR][1000 genomes]
rs451412	0.97[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs452789	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs453568	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs453933	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs454269	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs4669496	0.87[AFR][1000 genomes]
rs499858	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs514805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56010640	0.80[AFR][1000 genomes]
rs56102002	0.80[AFR][1000 genomes]
rs572907	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60508879	0.84[AFR][1000 genomes]
rs6731044	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599798	0.82[EUR][1000 genomes];1.00[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	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	nsv873628	chr2:9949464-9985670	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs287986	TAF1B	cis	Esophagus Muscularis	GTEx
rs287986	TAF1B	cis	lymphoblastoid	seeQTL
rs287986	RP11-95D17.1	cis	lung	GTEx
rs287986	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx
rs287986	TAF1B	cis	Nerve Tibial	GTEx
rs287986	KCNF1	cis	parietal	SCAN
rs287986	TAF1B	cis	cerebellum	SCAN
rs287986	TAF1B	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9984200-9986200	Weak transcription	Spleen	Spleen
2	chr2:9984200-9994000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:9984400-9986200	Weak transcription	Aorta	Aorta
4	chr2:9984400-9986400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:9984400-9987400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:9984600-9986000	Weak transcription	Esophagus	oesophagus
7	chr2:9984600-9986000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:9984600-9986200	Weak transcription	Fetal Intestine Large	intestine
9	chr2:9984600-9986200	Weak transcription	Left Ventricle	heart
10	chr2:9984600-9986400	Weak transcription	Gastric	stomach
11	chr2:9984600-9990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:9984600-9992600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:9984600-9995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:9984800-9985800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:9984800-9986000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:9984800-9997600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:9984800-9998400	Weak transcription	Pancreas	Pancrea
18	chr2:9985000-9985800	Enhancers	Primary T cells from cord blood	blood
19	chr2:9985000-9985800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:9985000-9986000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:9985000-9986000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:9985000-9986000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:9985000-9986000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:9985000-9986000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:9985000-9986000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:9985000-9986000	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:9985000-9986000	Genic enhancers	Fetal Thymus	thymus
28	chr2:9985000-9986200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:9985000-9986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:9985000-9986200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:9985000-9986200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:9985000-9986200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:9985000-9986200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:9985000-9986200	Weak transcription	Liver	Liver
35	chr2:9985000-9986200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:9985000-9986200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:9985000-9986200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:9985000-9986200	Enhancers	Placenta	Placenta
39	chr2:9985000-9986200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:9985000-9986200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:9985000-9986200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:9985000-9986200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:9985000-9986200	Enhancers	HepG2	liver
44	chr2:9985000-9987200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:9985000-9987200	Weak transcription	Psoas Muscle	Psoas
46	chr2:9985000-9990400	Weak transcription	Brain Angular Gyrus	brain
47	chr2:9985000-9990800	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:9985000-9991000	Weak transcription	Colonic Mucosa	Colon
49	chr2:9985000-9992000	Weak transcription	Brain Substantia Nigra	brain
50	chr2:9985000-9992000	Weak transcription	Lung	lung

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