Variant report

Variant	rs2297418
Chromosome Location	chr1:227192579-227192580
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227191783..227193581-chr1:227195403..227197131,2	K562	blood:
2	chr1:227173983..227176329-chr1:227192052..227193578,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1045252	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs1045285	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045286	0.87[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1045287	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045289	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1045290	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10495273	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10495274	0.80[MKK][hapmap]
rs10916075	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577007	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578103	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578479	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11580229	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11583229	0.89[ASN][1000 genomes]
rs11583489	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11586604	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11587443	0.81[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11588904	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589344	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1186	0.96[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12403236	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403775	0.90[CHB][hapmap]
rs12405857	0.89[ASN][1000 genomes]
rs12406714	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409230	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12409428	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410103	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12593	0.92[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1319103	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs1343743	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343744	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343745	0.99[ASN][1000 genomes]
rs17528667	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17592479	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17600627	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17600669	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17600725	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17600747	0.89[ASN][1000 genomes]
rs17600947	0.89[ASN][1000 genomes]
rs1929855	0.93[CHB][hapmap]
rs1929862	0.92[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1929863	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104860	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2183836	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2297412	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2297415	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2297416	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297419	0.99[ASN][1000 genomes]
rs3738725	0.96[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3738729	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768419	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768420	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3768421	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3768423	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768424	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3768425	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3795445	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795446	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795449	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795451	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3795453	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4146588	0.93[CHB][hapmap]
rs61834001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834004	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61834005	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61834006	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61834039	0.89[ASN][1000 genomes]
rs6426558	0.87[AMR][1000 genomes]
rs6426559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426560	0.89[ASN][1000 genomes]
rs6426584	0.93[CHB][hapmap]
rs6659424	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664955	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677602	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6684821	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690803	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6693535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699400	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6704144	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68087483	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7520272	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7535826	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541033	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549465	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7549586	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552783	0.80[AMR][1000 genomes]
rs7553837	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7555621	0.85[ASN][1000 genomes]
rs9726097	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727512	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2297418	CABC1	cis	parietal	SCAN
rs2297418	ADCK3	cis	Whole Blood	GTEx
rs2297418	SERPINA7	trans	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227175200-227198400	Weak transcription	A549	lung
3	chr1:227175200-227210200	Weak transcription	HMEC	breast
4	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:227176000-227216400	Weak transcription	NHLF	lung
6	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
7	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
8	chr1:227178600-227206600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:227179400-227198400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:227179400-227204400	Weak transcription	Stomach Mucosa	stomach
12	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
13	chr1:227179600-227213800	Weak transcription	NH-A	brain
14	chr1:227182000-227216000	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:227182200-227205600	Weak transcription	Fetal Brain Male	brain
16	chr1:227182600-227206400	Weak transcription	Brain Germinal Matrix	brain
17	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
18	chr1:227183200-227202600	Weak transcription	Pancreas	Pancrea
19	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
21	chr1:227183600-227204600	Weak transcription	HepG2	liver
22	chr1:227183800-227203000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:227184000-227203200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:227184000-227204200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:227184000-227214600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:227184000-227234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:227184200-227206600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:227184600-227208000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:227187200-227218600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:227187800-227192800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:227187800-227192800	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:227187800-227193400	Strong transcription	HUVEC	blood vessel
33	chr1:227187800-227194800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr1:227188000-227192800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:227188000-227194600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:227188200-227192800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:227188200-227192800	Strong transcription	Adipose Nuclei	Adipose
38	chr1:227188200-227192800	Strong transcription	Brain Anterior Caudate	brain
39	chr1:227188200-227192800	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr1:227188200-227192800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:227188200-227192800	Strong transcription	Fetal Intestine Large	intestine
42	chr1:227188200-227192800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:227188200-227192800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:227188200-227193000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:227188200-227194400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:227188200-227194400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:227188400-227192800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:227188400-227193000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:227188400-227193000	Strong transcription	Fetal Stomach	stomach
50	chr1:227188600-227192800	Strong transcription	Fetal Lung	lung

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