Variant report

Variant	rs12131061
Chromosome Location	chr1:227376308-227376309
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	chr1:227373675..227376391-chr1:227377073..227380557,3	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10495271	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs10495272	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs10916112	0.92[AMR][1000 genomes]
rs10916113	0.92[AMR][1000 genomes]
rs10916116	0.92[AMR][1000 genomes]
rs10916125	0.89[AMR][1000 genomes]
rs11576239	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11584325	0.85[AMR][1000 genomes]
rs11585910	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12117207	0.82[CEU][hapmap]
rs12119153	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs12119448	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12122759	0.87[CEU][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12123597	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12128174	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12131459	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12131913	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs12131933	0.92[AMR][1000 genomes]
rs12133230	0.92[AMR][1000 genomes]
rs12133633	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12138092	0.89[AMR][1000 genomes]
rs12138364	0.92[AMR][1000 genomes]
rs12138383	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12138664	0.92[AMR][1000 genomes]
rs12144205	0.92[AMR][1000 genomes]
rs12744825	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs12746316	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs12747807	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12751015	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs12754677	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12755770	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1320495	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs1513607	0.88[AMR][1000 genomes]
rs1513613	0.92[AMR][1000 genomes]
rs17545704	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs17546688	0.83[EUR][1000 genomes]
rs17601316	1.00[YRI][hapmap]
rs17613235	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2063661	0.92[AMR][1000 genomes]
rs28648445	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34113967	0.92[AMR][1000 genomes]
rs34702208	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34897490	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35160496	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35952573	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36133891	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3768422	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs3768431	1.00[YRI][hapmap]
rs4308948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61834323	0.92[AMR][1000 genomes]
rs61834324	0.92[AMR][1000 genomes]
rs61834326	0.92[AMR][1000 genomes]
rs61834590	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61834625	0.89[AMR][1000 genomes]
rs61834626	0.92[AMR][1000 genomes]
rs6660168	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6674640	1.00[YRI][hapmap]
rs6675572	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6678714	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6697583	0.89[AMR][1000 genomes]
rs7512871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7518813	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes]
rs7523759	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs7526822	0.87[CEU][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7533684	1.00[YRI][hapmap]
rs7539662	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes]
rs7543419	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs7548118	0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12131061	CNIH4	cis	cerebellum	SCAN
rs12131061	CABC1	cis	parietal	SCAN
rs12131061	PSEN2	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
4	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
6	chr1:227343200-227400400	Weak transcription	A549	lung
7	chr1:227346800-227379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
11	chr1:227347200-227378000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:227347800-227385800	Weak transcription	Fetal Intestine Small	intestine
13	chr1:227347800-227390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:227348200-227376400	Weak transcription	Fetal Lung	lung
15	chr1:227348200-227377800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:227348200-227377800	Weak transcription	HUVEC	blood vessel
17	chr1:227348200-227379800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:227348200-227398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:227348400-227378000	Weak transcription	Liver	Liver
24	chr1:227355400-227379800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:227355400-227386200	Weak transcription	Brain Anterior Caudate	brain
26	chr1:227359200-227379600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:227359400-227379800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:227359400-227379800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:227359400-227379800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:227359400-227389000	Weak transcription	Right Ventricle	heart
31	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
32	chr1:227362800-227377600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:227362800-227377800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:227362800-227379800	Weak transcription	NHLF	lung
35	chr1:227363000-227379600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:227363800-227380600	Weak transcription	Esophagus	oesophagus
37	chr1:227364000-227379800	Weak transcription	HSMMtube	muscle
38	chr1:227364000-227385800	Weak transcription	Fetal Stomach	stomach
39	chr1:227364200-227381000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:227365800-227399400	Weak transcription	Fetal Intestine Large	intestine
41	chr1:227369000-227379600	Weak transcription	HMEC	breast
42	chr1:227369200-227382600	Weak transcription	Fetal Brain Female	brain
43	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:227370600-227379400	Weak transcription	NHDF-Ad	bronchial
45	chr1:227370600-227380000	Weak transcription	Gastric	stomach
46	chr1:227370800-227377800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:227370800-227378200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:227371400-227378600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:227371400-227381000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:227371600-227380000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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