Variant report

Variant	rs12996459
Chromosome Location	chr2:152114548-152114549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152114220..152115726-chr2:152118400..152119936,2	K562	blood:
2	chr2:152106609..152109235-chr2:152114382..152116321,2	K562	blood:
3	chr2:152111081..152114725-chr2:152118123..152119862,3	MCF-7	breast:
4	chr2:152113115..152114989-chr2:152116609..152119218,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184898	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1048135	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11678123	0.84[ASN][1000 genomes]
rs11680338	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683487	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11691055	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11691217	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11730	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467046	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471191	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12476687	0.83[ASN][1000 genomes]
rs12624156	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693004	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12987765	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13001328	0.84[ASN][1000 genomes]
rs13004590	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015862	0.81[ASN][1000 genomes]
rs13020962	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025888	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13027425	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17798290	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2113508	0.90[ASN][1000 genomes]
rs2218880	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271811	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278090	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2880488	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs289904	0.86[EUR][1000 genomes]
rs289905	0.86[EUR][1000 genomes]
rs289906	0.89[EUR][1000 genomes]
rs289907	0.86[EUR][1000 genomes]
rs289921	0.86[EUR][1000 genomes]
rs289923	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs289924	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34028108	0.92[ASN][1000 genomes]
rs34452578	0.86[ASN][1000 genomes]
rs34538548	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35659175	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35723696	0.84[ASN][1000 genomes]
rs35863408	0.84[ASN][1000 genomes]
rs3771882	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3854012	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856557	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664336	0.84[ASN][1000 genomes]
rs4664347	0.84[ASN][1000 genomes]
rs4664349	0.84[ASN][1000 genomes]
rs4665051	0.91[AFR][1000 genomes]
rs4665114	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665137	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4665150	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4665168	0.93[ASN][1000 genomes]
rs55775354	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56335263	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56376752	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57201382	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66521733	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66588921	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67303849	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6739517	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67725431	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558169	0.84[ASN][1000 genomes]
rs7559296	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7574228	0.84[ASN][1000 genomes]
rs7587037	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[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	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1014936	chr2:152019809-152118479	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12996459	TNFAIP6	cis	Whole Blood	GTEx
rs12996459	NMI	Cis_1M	lymphoblastoid	RTeQTL
rs12996459	TNFAIP6	cis	Muscle Skeletal	GTEx
rs12996459	RBM43	cis	Whole Blood	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152094400-152117000	Weak transcription	A549	lung
2	chr2:152101600-152117200	Weak transcription	Fetal Kidney	kidney
3	chr2:152102000-152116600	Weak transcription	Pancreas	Pancrea
4	chr2:152103400-152117600	Weak transcription	Gastric	stomach
5	chr2:152103800-152117600	Weak transcription	Esophagus	oesophagus
6	chr2:152104400-152117200	Weak transcription	Colonic Mucosa	Colon
7	chr2:152104600-152117200	Weak transcription	Stomach Mucosa	stomach
8	chr2:152105800-152114600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:152105800-152116800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:152105800-152116800	Weak transcription	K562	blood
11	chr2:152105800-152117200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:152105800-152117200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:152106400-152116800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:152106400-152117200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:152106400-152117200	Weak transcription	Brain Substantia Nigra	brain
16	chr2:152106400-152117600	Weak transcription	Left Ventricle	heart
17	chr2:152106600-152116800	Weak transcription	HUVEC	blood vessel
18	chr2:152106600-152117000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:152106600-152117000	Weak transcription	Brain Anterior Caudate	brain
20	chr2:152106600-152117200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:152106600-152117200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:152106600-152117200	Weak transcription	Fetal Intestine Large	intestine
23	chr2:152106600-152117400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:152106800-152117000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:152107400-152116800	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:152107600-152117000	Weak transcription	Brain Angular Gyrus	brain
27	chr2:152108000-152114600	Weak transcription	HSMMtube	muscle
28	chr2:152108000-152117000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:152108000-152117200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:152108000-152117200	Weak transcription	HSMM	muscle
31	chr2:152108200-152114600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:152108200-152117000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:152108200-152117000	Weak transcription	NHDF-Ad	bronchial
34	chr2:152108400-152116600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:152108400-152116800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:152108400-152117000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:152108400-152117000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:152108400-152117200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:152108600-152117000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:152109000-152116600	Weak transcription	Placenta	Placenta
41	chr2:152109000-152116600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:152109000-152117000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:152109000-152117200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:152109200-152117200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:152109400-152117000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:152109800-152116800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr2:152109800-152117000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:152109800-152117600	Weak transcription	Spleen	Spleen
49	chr2:152110000-152114600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:152110400-152116800	Weak transcription	Primary hematopoietic stem cells	blood

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