Variant report

Variant	rs12405857
Chromosome Location	chr1:227208970-227208971
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	chr1:227203892..227205446-chr1:227206792..227208982,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10127638	0.86[CEU][hapmap]
rs1045285	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs1045287	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10495256	0.86[CEU][hapmap]
rs10916075	0.89[ASN][1000 genomes]
rs11577007	0.89[ASN][1000 genomes]
rs11578103	0.89[ASN][1000 genomes]
rs11578479	0.99[ASN][1000 genomes]
rs11580229	0.99[ASN][1000 genomes]
rs11582863	0.83[ASN][1000 genomes]
rs11583229	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583489	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11588329	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11588904	0.89[ASN][1000 genomes]
rs12403236	0.89[ASN][1000 genomes]
rs12403775	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs12406714	0.89[ASN][1000 genomes]
rs12409230	0.84[ASN][1000 genomes]
rs12409428	0.89[ASN][1000 genomes]
rs12409755	0.89[ASN][1000 genomes]
rs12410103	0.89[ASN][1000 genomes]
rs12593	0.93[CHB][hapmap]
rs1319103	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs13376552	0.83[ASN][1000 genomes]
rs1343743	0.89[ASN][1000 genomes]
rs1343744	0.89[ASN][1000 genomes]
rs1343745	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17600725	0.99[ASN][1000 genomes]
rs17600747	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929855	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs1929863	0.89[ASN][1000 genomes]
rs1929864	0.89[ASN][1000 genomes]
rs2104860	0.99[ASN][1000 genomes]
rs2297413	0.91[EUR][1000 genomes]
rs2297415	0.88[ASN][1000 genomes]
rs2297416	0.87[ASN][1000 genomes]
rs2297418	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2297419	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2802271	0.85[CEU][hapmap]
rs34111989	0.83[ASN][1000 genomes]
rs3738729	0.89[ASN][1000 genomes]
rs3768419	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3768420	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3768423	0.89[ASN][1000 genomes]
rs3795445	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3795446	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3795449	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3795453	0.99[ASN][1000 genomes]
rs4146588	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs61834001	0.89[ASN][1000 genomes]
rs61834006	0.91[ASN][1000 genomes]
rs61834039	0.97[ASN][1000 genomes]
rs6426559	0.89[ASN][1000 genomes]
rs6426560	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426584	0.86[CHB][hapmap]
rs6659424	0.86[ASN][1000 genomes]
rs6664955	0.89[ASN][1000 genomes]
rs6670924	0.89[ASN][1000 genomes]
rs6677602	0.93[CHB][hapmap]
rs6684821	0.89[ASN][1000 genomes]
rs6693535	0.89[ASN][1000 genomes]
rs72748192	0.83[ASN][1000 genomes]
rs7355000	0.83[ASN][1000 genomes]
rs7535826	0.99[ASN][1000 genomes]
rs7541033	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs7549465	0.94[ASN][1000 genomes]
rs7549586	0.99[ASN][1000 genomes]
rs7553837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7553990	0.83[ASN][1000 genomes]
rs7555621	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs938257	0.86[CEU][hapmap]
rs9726097	0.89[ASN][1000 genomes]
rs9727512	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1005811	chr1:227196502-227215967	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1007352	chr1:227196502-227247160	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv997751	chr1:227196502-227263537	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1010864	chr1:227199493-227246753	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1014423	chr1:227201253-227268843	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227175200-227210200	Weak transcription	HMEC	breast
3	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:227176000-227216400	Weak transcription	NHLF	lung
5	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
6	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
7	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
9	chr1:227179600-227213800	Weak transcription	NH-A	brain
10	chr1:227182000-227216000	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
12	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
14	chr1:227184000-227214600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:227184000-227234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:227187200-227218600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:227190600-227217000	Weak transcription	Esophagus	oesophagus
18	chr1:227190600-227223200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:227190600-227272600	Weak transcription	Lung	lung
20	chr1:227191200-227214400	Weak transcription	Aorta	Aorta
21	chr1:227192600-227220200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:227192800-227214200	Weak transcription	Right Ventricle	heart
23	chr1:227192800-227220200	Weak transcription	Gastric	stomach
24	chr1:227201400-227210800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:227202200-227209200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:227202400-227209000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:227202600-227209000	Strong transcription	Brain Hippocampus Middle	brain
28	chr1:227202600-227217200	Strong transcription	Adipose Nuclei	Adipose
29	chr1:227202600-227222600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:227203000-227209000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
32	chr1:227203200-227209200	Strong transcription	HUVEC	blood vessel
33	chr1:227204400-227209400	Strong transcription	HSMMtube	muscle
34	chr1:227204800-227214400	Weak transcription	Brain Substantia Nigra	brain
35	chr1:227205000-227210400	Weak transcription	NHDF-Ad	bronchial
36	chr1:227205000-227210600	Strong transcription	Fetal Intestine Large	intestine
37	chr1:227205400-227216400	Weak transcription	HepG2	liver
38	chr1:227205600-227209200	Strong transcription	Fetal Kidney	kidney
39	chr1:227205600-227220400	Weak transcription	Stomach Mucosa	stomach
40	chr1:227205800-227209200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:227205800-227210600	Strong transcription	Left Ventricle	heart
42	chr1:227206000-227209000	Strong transcription	Brain Anterior Caudate	brain
43	chr1:227206000-227209200	Strong transcription	Fetal Lung	lung
44	chr1:227206000-227209400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:227206000-227210600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:227206200-227209000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr1:227206200-227210800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr1:227206400-227209000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:227206400-227209000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
50	chr1:227206400-227209400	Strong transcription	Sigmoid Colon	Sigmoid Colon

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