Variant report

Variant	rs2279665
Chromosome Location	chr12:56827694-56827695
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56827122..56829878-chr12:56841273..56843034,2	K562	blood:
2	chr12:56827122..56829045-chr12:56841534..56843254,2	K562	blood:
3	chr12:56822652..56825440-chr12:56826131..56828789,2	MCF-7	breast:
4	chr12:56816330..56820698-chr12:56827397..56831177,4	K562	blood:
5	chr12:56827605..56830208-chr12:56835234..56837438,3	K562	blood:

Variant related genes	Relation type
ENSG00000111602	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10876889	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876890	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171847	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171848	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171849	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171850	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171852	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171856	0.82[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs11610921	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11833581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11833583	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12299614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12313431	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12316810	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12815993	0.90[ASN][1000 genomes]
rs1976294	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291738	0.92[CEU][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2291739	0.93[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2371455	0.82[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs2638304	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657883	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2939303	0.82[ASN][1000 genomes]
rs34520497	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34644700	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35634983	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782237	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809125	0.82[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs6581094	0.95[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581095	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67027355	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302060	0.80[EUR][1000 genomes]
rs7305989	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7312888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774026	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774031	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774032	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774037	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7977477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs812278	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs812279	0.92[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2279665	NACA	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56799400-56831600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56805800-56828200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:56806000-56831200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:56806800-56828200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:56807000-56827800	Strong transcription	Fetal Muscle Leg	muscle
6	chr12:56807200-56828200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:56807200-56829000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:56807400-56828000	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr12:56807400-56828000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:56807600-56828000	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr12:56807600-56828000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:56807600-56828000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:56807600-56828200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:56809200-56828000	Strong transcription	Fetal Thymus	thymus
15	chr12:56809200-56828600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:56809600-56828000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:56809800-56827800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:56809800-56827800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:56809800-56829000	Strong transcription	Dnd41	blood
20	chr12:56810000-56828000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:56810000-56828800	Weak transcription	Small Intestine	intestine
22	chr12:56810000-56829400	Weak transcription	Brain Substantia Nigra	brain
23	chr12:56810200-56828000	Strong transcription	A549	lung
24	chr12:56810200-56829400	Weak transcription	HSMMtube	muscle
25	chr12:56811400-56828200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:56811800-56830400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:56811800-56842400	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:56813000-56842600	Weak transcription	Fetal Heart	heart
29	chr12:56813200-56841200	Weak transcription	Fetal Kidney	kidney
30	chr12:56813800-56842400	Weak transcription	Right Atrium	heart
31	chr12:56814000-56827800	Strong transcription	NHEK	skin
32	chr12:56814000-56828000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:56816200-56842400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:56816600-56836400	Weak transcription	HMEC	breast
35	chr12:56816800-56828600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr12:56817400-56828000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:56817400-56829000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:56817600-56829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:56818600-56829600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:56818800-56833200	Weak transcription	Left Ventricle	heart
41	chr12:56819200-56829000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:56819400-56829400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:56819600-56828800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:56820200-56829400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:56820600-56827800	Strong transcription	Fetal Intestine Small	intestine
46	chr12:56820600-56827800	Strong transcription	Fetal Stomach	stomach
47	chr12:56820600-56828000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr12:56820800-56827800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:56820800-56827800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:56820800-56827800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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