Variant report

Variant	rs287996
Chromosome Location	chr2:9998168-9998169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:9982413..9984007-chr2:9997809..10000027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11692193	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008782	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs287972	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287974	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs287986	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287987	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287988	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287992	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287993	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287994	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287995	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287997	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287999	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382747	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs388570	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447465	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs451412	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669496	0.82[EUR][1000 genomes]
rs514805	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572907	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731044	1.00[ASN][1000 genomes]
rs7599798	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	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
9	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs287996	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx
rs287996	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs287996	TAF1B	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9984800-9998400	Weak transcription	Pancreas	Pancrea
2	chr2:9985000-10000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:9987200-10038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:9987400-10003200	Weak transcription	Stomach Mucosa	stomach
5	chr2:9987600-9998400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:9989200-9998200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:9989400-9998200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:9989400-9998400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:9989400-9999200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:9989400-10000600	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr2:9989400-10001000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr2:9989600-9998400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:9989600-9998400	Strong transcription	Adipose Nuclei	Adipose
14	chr2:9989600-9999200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:9989600-9999400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:9989600-10001200	Strong transcription	Osteobl	bone
17	chr2:9989800-9998200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:9989800-9999200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:9990000-9998600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:9990200-9998800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:9990400-10000600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr2:9990400-10000800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:9990600-9998400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:9990600-9998400	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:9990600-9998600	Strong transcription	Brain Anterior Caudate	brain
26	chr2:9990600-9999200	Strong transcription	Left Ventricle	heart
27	chr2:9990600-10000800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr2:9990600-10001600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:9990800-9999000	Strong transcription	Brain Hippocampus Middle	brain
30	chr2:9991000-9998800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:9992000-9998600	Strong transcription	Ovary	ovary
32	chr2:9992000-9999000	Strong transcription	Brain Cingulate Gyrus	brain
33	chr2:9992200-9998200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:9993000-10003600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:9993200-10001200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:9993600-10007400	Weak transcription	Psoas Muscle	Psoas
37	chr2:9993800-10002600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
38	chr2:9993800-10002800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:9993800-10079600	Weak transcription	Gastric	stomach
40	chr2:9994600-10000600	Weak transcription	Right Ventricle	heart
41	chr2:9994800-9998200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr2:9995000-9998200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:9995400-9999000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
44	chr2:9995400-10001200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
45	chr2:9995400-10002600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:9995400-10002800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:9995600-10002600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
48	chr2:9995800-10001200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
49	chr2:9995800-10001400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr2:9995800-10038000	Weak transcription	Small Intestine	intestine

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