Variant report

Variant	rs12194407
Chromosome Location	chr6:56975742-56975743
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	chr6:56975731..56978915-chr6:56980133..56983784,4	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1020550	0.90[ASN][1000 genomes]
rs10456192	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10484410	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11398	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12190575	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192222	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194288	0.90[ASN][1000 genomes]
rs12198801	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201039	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211901	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12214119	0.93[EUR][1000 genomes]
rs12214882	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411578	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16888392	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17619360	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800018	0.90[ASN][1000 genomes]
rs3800023	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800025	0.90[ASN][1000 genomes]
rs3957366	0.84[EUR][1000 genomes]
rs3996934	0.90[ASN][1000 genomes]
rs3996935	0.90[ASN][1000 genomes]
rs3996936	0.90[ASN][1000 genomes]
rs4523090	0.90[ASN][1000 genomes]
rs4631287	0.90[ASN][1000 genomes]
rs6459178	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902125	0.85[ASN][1000 genomes]
rs6918222	0.84[EUR][1000 genomes]
rs6936506	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72868608	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73463742	0.80[ASN][1000 genomes]
rs7744148	0.90[ASN][1000 genomes]
rs7748120	0.90[ASN][1000 genomes]
rs7748453	0.90[ASN][1000 genomes]
rs7753547	0.90[ASN][1000 genomes]
rs7756421	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7764446	0.90[ASN][1000 genomes]
rs7771115	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349841	0.85[ASN][1000 genomes]
rs9396247	0.85[ASN][1000 genomes]
rs9396256	0.90[ASN][1000 genomes]
rs986245	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12194407	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs12194407	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs12194407	BEND6	cis	Muscle Skeletal	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56958200-56979600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:56966600-56987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:56966600-56987600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:56966600-57012400	Weak transcription	Spleen	Spleen
5	chr6:56966800-56987600	Weak transcription	Fetal Intestine Small	intestine
6	chr6:56966800-57018000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:56967000-56979000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:56967000-56981600	Weak transcription	Stomach Mucosa	stomach
9	chr6:56967000-56983400	Weak transcription	Fetal Stomach	stomach
10	chr6:56967200-56979400	Weak transcription	Fetal Heart	heart
11	chr6:56967200-56992200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:56967600-56981400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:56967800-56976800	Weak transcription	Lung	lung
14	chr6:56967800-56992400	Weak transcription	A549	lung
15	chr6:56967800-56995400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:56967800-56995800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:56968000-56981600	Weak transcription	Ovary	ovary
18	chr6:56968000-56987800	Weak transcription	Aorta	Aorta
19	chr6:56968000-56993400	Weak transcription	Liver	Liver
20	chr6:56968000-56993600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:56968200-56986400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:56968200-56987000	Weak transcription	Fetal Intestine Large	intestine
23	chr6:56968200-57036400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr6:56968400-56993200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:56968400-57000800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:56968600-56977000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:56968600-56977200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:56968600-56987800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:56968600-56987800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:56968600-56998200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:56968600-57002200	Weak transcription	Thymus	Thymus
32	chr6:56968600-57006600	Weak transcription	Brain Angular Gyrus	brain
33	chr6:56968600-57018400	Weak transcription	Psoas Muscle	Psoas
34	chr6:56969000-56986600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:56969200-56986600	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:56969200-56987200	Weak transcription	Adipose Nuclei	Adipose
37	chr6:56969200-56987600	Weak transcription	Left Ventricle	heart
38	chr6:56969200-56987800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:56969200-56995400	Weak transcription	Brain Anterior Caudate	brain
40	chr6:56969200-56997800	Weak transcription	Fetal Lung	lung
41	chr6:56969400-56981600	Weak transcription	HSMMtube	muscle
42	chr6:56969400-56987800	Weak transcription	Fetal Thymus	thymus
43	chr6:56969400-56993600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:56969400-56997400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:56969400-56997800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:56969600-56983400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:56969600-56987600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:56969600-56990400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr6:56969600-56997600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:56969600-56999000	Weak transcription	Brain Inferior Temporal Lobe	brain

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