Variant report

Variant	rs12577418
Chromosome Location	chr11:17101554-17101555
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:17093738-17102258	K562	blood:	n/a	n/a
2	POLR2A	chr11:17101340-17102176	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:17101447-17101554	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:17101538-17101799	MCF-7	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:17101515..17104437-chr11:17228294..17230194,2	K562	blood:
2	chr11:17099951..17102029-chr11:17121087..17123839,2	MCF-7	breast:
3	chr11:17099995..17101561-chr11:17159735..17162103,2	K562	blood:
4	chr11:17099157..17100919-chr11:17101285..17103646,3	MCF-7	breast:
5	chr11:17100780..17101705-chr4:146653692..146654639,2	HCT-116	colon:
6	chr11:17097208..17101887-chr11:17227768..17230798,9	K562	blood:
7	chr11:17097048..17102595-chr11:17228016..17231208,7	MCF-7	breast:
8	chr11:17008798..17010671-chr11:17099542..17102207,2	MCF-7	breast:
9	chr11:17101306..17104344-chr11:17107893..17110404,3	MCF-7	breast:
10	chr11:17099359..17101768-chr11:17550989..17553473,2	K562	blood:
11	chr11:17101543..17103422-chr11:17105398..17108951,3	K562	blood:

No data

Variant related genes	Relation type
SNORD14B	TF binding region
RPS13	TF binding region
ENSG00000070081	Chromatin interaction
ENSG00000240808	Chromatin interaction
ENSG00000011405	Chromatin interaction
ENSG00000110700	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10832731	0.90[EUR][1000 genomes]
rs11024149	0.88[EUR][1000 genomes]
rs11024151	0.84[EUR][1000 genomes]
rs11608038	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1236311	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12420958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12575466	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12577388	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794156	0.86[ASN][1000 genomes]
rs17472942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17560341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561348	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17641418	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1987694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs214091	0.82[JPT][hapmap]
rs214903	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs214932	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs214933	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs214934	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs214938	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34724588	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34941502	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3950680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs476890	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs492263	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs522619	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56030184	0.85[ASN][1000 genomes]
rs569780	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs586785	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs615424	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61879692	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644419	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs664382	0.86[EUR][1000 genomes]
rs665311	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs679201	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7108067	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7478986	0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[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	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12577418	NUCB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17100000-17110800	Weak transcription	Stomach Mucosa	stomach
2	chr11:17100000-17111200	Weak transcription	Aorta	Aorta
3	chr11:17100000-17112800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:17100000-17112800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:17100200-17108000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:17100200-17109000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr11:17100200-17109400	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:17100200-17109800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:17100200-17109800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:17100200-17109800	Weak transcription	Left Ventricle	heart
11	chr11:17100200-17110000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:17100200-17110000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:17100200-17110000	Weak transcription	Ovary	ovary
14	chr11:17100200-17110200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:17100200-17110200	Weak transcription	Fetal Kidney	kidney
16	chr11:17100200-17110200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr11:17100200-17110200	Weak transcription	HSMMtube	muscle
18	chr11:17100200-17110600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:17100200-17110600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:17100200-17110600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr11:17100200-17110800	Weak transcription	Fetal Lung	lung
22	chr11:17100200-17111200	Weak transcription	Fetal Stomach	stomach
23	chr11:17100200-17112200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:17100200-17112400	Weak transcription	Psoas Muscle	Psoas
25	chr11:17100200-17112600	Weak transcription	NHLF	lung
26	chr11:17100200-17113200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:17100200-17115000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr11:17100400-17106600	Weak transcription	NH-A	brain
29	chr11:17100400-17106800	Weak transcription	Fetal Intestine Small	intestine
30	chr11:17100400-17107000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:17100400-17108200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:17100400-17108200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:17100400-17108400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:17100400-17108600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr11:17100400-17108800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:17100400-17109000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:17100400-17109000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:17100400-17109000	Weak transcription	Brain Anterior Caudate	brain
39	chr11:17100400-17109000	Weak transcription	NHDF-Ad	bronchial
40	chr11:17100400-17109200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:17100400-17110000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:17100400-17110000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr11:17100400-17110200	Weak transcription	Primary T cells from cord blood	blood
44	chr11:17100400-17110200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:17100400-17110200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:17100400-17110200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:17100400-17110200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr11:17100400-17110200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:17100400-17110200	Weak transcription	Brain Angular Gyrus	brain
50	chr11:17100400-17110200	Weak transcription	Brain Hippocampus Middle	brain

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