Variant report

Variant	rs12299614
Chromosome Location	chr12:56831182-56831183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56708477..56711589-chr12:56829943..56832249,3	K562	blood:
2	chr12:56831091..56839552-chr12:56841407..56847301,11	K562	blood:
3	chr12:56816366..56820011-chr12:56829116..56832122,4	K562	blood:
4	chr12:56831181..56832925-chr12:56855832..56858189,2	K562	blood:
5	chr12:56827738..56829538-chr12:56829816..56833638,4	K562	blood:
6	chr12:56727279..56730018-chr12:56830009..56833099,3	K562	blood:
7	chr12:56811830..56813954-chr12:56828376..56831267,3	K562	blood:

Variant related genes	Relation type
ENSG00000257727	Chromatin interaction
ENSG00000111602	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000135473	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];0.95[ASN][1000 genomes]
rs10876890	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171847	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171848	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171849	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171850	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171852	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171856	0.82[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs11610921	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11833581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833583	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12313431	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12316810	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12815993	0.92[ASN][1000 genomes]
rs1976294	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279665	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]
rs2291738	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2291739	0.93[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs2371455	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs2638304	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2657883	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs2939303	0.84[ASN][1000 genomes]
rs34520497	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34644700	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35634983	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782237	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809125	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs6581094	0.95[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581095	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67027355	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302060	0.81[EUR][1000 genomes]
rs7305989	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[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];0.97[ASN][1000 genomes]
rs774026	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774031	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774032	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774037	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs812278	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs812279	0.92[CEU][hapmap];0.89[TSI][hapmap];0.87[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
rs12299614	NACA	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56799400-56831600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56806000-56831200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:56811800-56842400	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:56813000-56842600	Weak transcription	Fetal Heart	heart
5	chr12:56813200-56841200	Weak transcription	Fetal Kidney	kidney
6	chr12:56813800-56842400	Weak transcription	Right Atrium	heart
7	chr12:56816200-56842400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:56816600-56836400	Weak transcription	HMEC	breast
9	chr12:56818800-56833200	Weak transcription	Left Ventricle	heart
10	chr12:56822600-56836000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:56822800-56836200	Weak transcription	Colonic Mucosa	Colon
12	chr12:56822800-56838000	Weak transcription	HUVEC	blood vessel
13	chr12:56824800-56831400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:56825000-56833000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:56825400-56842000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:56825800-56836600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:56826200-56842400	Weak transcription	NH-A	brain
18	chr12:56826400-56841800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:56826400-56842200	Weak transcription	HSMM	muscle
20	chr12:56826400-56842400	Weak transcription	NHDF-Ad	bronchial
21	chr12:56827200-56831200	Weak transcription	Brain Anterior Caudate	brain
22	chr12:56827200-56842600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:56827600-56831200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:56827600-56831400	Weak transcription	Fetal Lung	lung
25	chr12:56827600-56836000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:56827800-56831400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:56827800-56836000	Weak transcription	NHEK	skin
28	chr12:56827800-56836800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:56827800-56836800	Weak transcription	Fetal Intestine Small	intestine
30	chr12:56827800-56837800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:56827800-56841200	Weak transcription	HepG2	liver
32	chr12:56827800-56841800	Weak transcription	Primary B cells from cord blood	blood
33	chr12:56827800-56841800	Weak transcription	Lung	lung
34	chr12:56827800-56842200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:56827800-56842400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:56827800-56842400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:56827800-56842400	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:56827800-56842400	Weak transcription	Fetal Stomach	stomach
39	chr12:56827800-56842400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:56827800-56842600	Weak transcription	Spleen	Spleen
41	chr12:56828000-56831200	Weak transcription	Primary T cells from cord blood	blood
42	chr12:56828000-56831400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:56828000-56831400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:56828000-56831800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr12:56828000-56835000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:56828000-56836000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:56828000-56836000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:56828000-56836200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:56828000-56836400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:56828000-56841200	Weak transcription	A549	lung

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