Variant report

Variant	rs6679980
Chromosome Location	chr1:211433672-211433673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:210543442..210549646-chr1:211430130..211435518,10	MCF-7	breast:
2	chr1:211431689..211435313-chr1:211451941..211455577,4	K562	blood:
3	chr1:211432252..211434880-chr1:211475465..211477456,2	K562	blood:
4	chr1:210545161..210548943-chr1:211431162..211434734,10	MCF-7	breast:
5	chr1:210546304..210548726-chr1:211433366..211435093,2	K562	blood:
6	chr1:211432764..211434575-chr1:211756364..211758782,2	K562	blood:
7	chr1:211429664..211434083-chr1:211498779..211503937,6	K562	blood:
8	chr1:211430859..211434419-chr1:211555069..211558654,5	K562	blood:
9	chr1:211429664..211435180-chr1:211498779..211503937,6	K562	blood:
10	chr1:210545931..210548726-chr1:211432289..211435093,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000082512	Chromatin interaction
ENSG00000153363	Chromatin interaction
ENSG00000117625	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000261314	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11119713	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11803005	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11806910	0.88[EUR][1000 genomes]
rs12723208	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12729996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731366	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs12743163	0.88[CEU][hapmap]
rs12743458	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752670	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs12754607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754747	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756590	0.94[EUR][1000 genomes]
rs17188916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17188937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189000	0.83[TSI][hapmap]
rs17267484	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs17267491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17267554	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs17267561	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2280079	1.00[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs34027321	0.98[EUR][1000 genomes]
rs34140425	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34251608	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34256746	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34813082	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35228985	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35374835	0.80[EUR][1000 genomes]
rs35711226	0.85[EUR][1000 genomes]
rs35791308	0.87[EUR][1000 genomes]
rs35995968	0.93[EUR][1000 genomes]
rs3738200	0.83[TSI][hapmap]
rs41275358	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540681	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs66526219	0.94[EUR][1000 genomes]
rs6686281	0.85[EUR][1000 genomes]
rs67437198	0.80[EUR][1000 genomes]
rs67764962	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67772854	0.87[EUR][1000 genomes]
rs71640006	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7556054	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343270	chr1:211431354-211434202	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv3352231	chr1:211431654-211434427	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv3373410	chr1:211432129-211434077	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6679980	RCOR3	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211430600-211434600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:211430600-211434600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr1:211430800-211434600	Active TSS	Aorta	Aorta
4	chr1:211431000-211434400	Active TSS	Brain Anterior Caudate	brain
5	chr1:211431000-211434400	Active TSS	NHLF	lung
6	chr1:211431000-211434800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:211431000-211434800	Active TSS	Fetal Intestine Large	intestine
8	chr1:211431200-211434200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:211431200-211434200	Active TSS	Fetal Muscle Trunk	muscle
10	chr1:211431200-211434200	Active TSS	Fetal Muscle Leg	muscle
11	chr1:211431200-211434400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:211431200-211434400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:211431200-211434400	Active TSS	Placenta Amnion	Placenta Amnion
14	chr1:211431200-211434600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:211431200-211434600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:211431200-211434600	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr1:211431200-211434600	Active TSS	Fetal Stomach	stomach
18	chr1:211431200-211434600	Active TSS	K562	blood
19	chr1:211431200-211434800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:211431200-211434800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:211431200-211434800	Active TSS	Fetal Intestine Small	intestine
22	chr1:211431200-211435000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:211431400-211433800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:211431400-211434400	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr1:211431400-211434400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:211431400-211434400	Active TSS	Colonic Mucosa	Colon
27	chr1:211431400-211434400	Active TSS	Colon Smooth Muscle	Colon
28	chr1:211431400-211434400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:211431400-211434400	Active TSS	Fetal Heart	heart
30	chr1:211431400-211434400	Active TSS	Fetal Kidney	kidney
31	chr1:211431400-211434400	Active TSS	Fetal Lung	lung
32	chr1:211431400-211434400	Active TSS	Lung	lung
33	chr1:211431400-211434600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:211431400-211434600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:211431400-211434600	Active TSS	Ovary	ovary
36	chr1:211431400-211434600	Active TSS	Pancreas	Pancrea
37	chr1:211431400-211434600	Active TSS	Rectal Smooth Muscle	rectum
38	chr1:211431400-211434600	Active TSS	Thymus	Thymus
39	chr1:211431400-211434600	Active TSS	HSMMtube	muscle
40	chr1:211431400-211434800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:211431400-211434800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:211431400-211434800	Active TSS	Left Ventricle	heart
43	chr1:211431400-211434800	Active TSS	Psoas Muscle	Psoas
44	chr1:211431400-211434800	Active TSS	Right Ventricle	heart
45	chr1:211431400-211435000	Active TSS	NHDF-Ad	bronchial
46	chr1:211431600-211434400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:211431600-211434400	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr1:211431600-211434400	Active TSS	Fetal Brain Male	brain
49	chr1:211431600-211434400	Active TSS	Gastric	stomach
50	chr1:211431600-211434400	Active TSS	Sigmoid Colon	Sigmoid Colon

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