Variant report

Variant	rs16867203
Chromosome Location	chr2:9996623-9996624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9995313..9997002-chr2:10028213..10029998,2	MCF-7	breast:
2	chr2:9990181..9994001-chr2:9995377..9997163,3	MCF-7	breast:
3	chr2:9980973..9983843-chr2:9994187..9996766,3	K562	blood:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1119632	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs1119633	0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11887231	0.88[ASN][1000 genomes]
rs13404815	0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs13429581	0.88[ASN][1000 genomes]
rs16867192	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1971101	0.85[CHB][hapmap]
rs2245344	0.85[CHB][hapmap]
rs2303914	0.85[CHB][hapmap]
rs2656329	0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287975	0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287976	0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287977	0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287978	0.88[ASN][1000 genomes]
rs287979	0.88[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287980	0.89[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287981	0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287982	0.89[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs287983	0.82[MEX][hapmap]
rs2884174	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]
rs56154233	0.88[ASN][1000 genomes]
rs57352580	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58521916	0.88[ASN][1000 genomes]
rs6432044	0.85[CHB][hapmap]
rs72780999	0.95[ASN][1000 genomes]
rs72782605	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72782633	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72782634	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782637	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16867203	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs16867203	CMPK2	cis	parietal	SCAN
rs16867203	ADAM17	cis	cerebellum	SCAN
rs16867203	RRM2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9984800-9997600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:9984800-9998400	Weak transcription	Pancreas	Pancrea
3	chr2:9985000-10000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:9985200-9997200	Weak transcription	Fetal Heart	heart
5	chr2:9985600-9997200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:9985800-9997000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:9986200-9997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:9987200-10038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:9987400-9997400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:9987400-10003200	Weak transcription	Stomach Mucosa	stomach
11	chr2:9987600-9997000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:9987600-9998400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:9989000-9997200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:9989000-9997200	Strong transcription	K562	blood
15	chr2:9989000-9997800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:9989000-9997800	Strong transcription	HUVEC	blood vessel
17	chr2:9989000-9997800	Strong transcription	NH-A	brain
18	chr2:9989200-9997000	Strong transcription	HepG2	liver
19	chr2:9989200-9997600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:9989200-9998200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:9989400-9997600	Strong transcription	NHDF-Ad	bronchial
22	chr2:9989400-9997800	Strong transcription	Fetal Thymus	thymus
23	chr2:9989400-9998200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:9989400-9998400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:9989400-9999200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:9989400-10000600	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr2:9989400-10001000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr2:9989600-9997400	Strong transcription	HSMM	muscle
29	chr2:9989600-9997600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr2:9989600-9997800	Strong transcription	Liver	Liver
31	chr2:9989600-9998400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:9989600-9998400	Strong transcription	Adipose Nuclei	Adipose
33	chr2:9989600-9999200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:9989600-9999400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:9989600-10001200	Strong transcription	Osteobl	bone
36	chr2:9989800-9996800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:9989800-9997400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:9989800-9997800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:9989800-9998200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr2:9989800-9999200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:9990000-9996800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:9990000-9997400	Strong transcription	Fetal Lung	lung
43	chr2:9990000-9997600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr2:9990000-9997800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:9990000-9997800	Strong transcription	Placenta	Placenta
46	chr2:9990000-9998000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:9990000-9998600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:9990200-9998800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:9990400-10000600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr2:9990400-10000800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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