Variant report

Variant	rs10840243
Chromosome Location	chr11:9483493-9483494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:123)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:123 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:9480308-9483702	PFSK-1	brain:	n/a	n/a
2	MXI1	chr11:9481736-9483787	Hela-S3	cervix:	n/a	chr11:9481818-9481833
3	TAL1	chr11:9481931-9483851	K562	blood:	n/a	n/a
4	POLR2A	chr11:9483379-9483641	GM12891	blood:	n/a	n/a
5	MAFK	chr11:9483405-9483798	IMR90	lung:	n/a	n/a
6	POLR2A	chr11:9480817-9484127	GM18505	blood:	n/a	n/a
7	POLR2A	chr11:9480875-9483890	U87	brain:	n/a	n/a
8	POLR2A	chr11:9481042-9483691	HL-60	blood:	n/a	n/a
9	TBP	chr11:9481249-9483906	Hela-S3	cervix:	n/a	n/a
10	FOXM1	chr11:9481183-9483652	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:9481141-9483836	GM18951	blood:	n/a	n/a
12	POLR2A	chr11:9483319-9483804	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr11:9480878-9483810	HCT-116	colon:	n/a	n/a
14	POLR2A	chr11:9481144-9483699	ProgFib	skin:	n/a	n/a
15	RCOR1	chr11:9481963-9483635	K562	blood:	n/a	n/a
16	POLR2A	chr11:9480642-9483619	K562	blood:	n/a	n/a
17	TBL1XR1	chr11:9482007-9483686	K562	blood:	n/a	n/a
18	GATA2	chr11:9483339-9483600	SH-SY5Y	brain:	n/a	n/a
19	POLR2A	chr11:9481131-9483713	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr11:9480818-9483893	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr11:9483337-9483718	GM12878	blood:	n/a	n/a
22	NFIC	chr11:9481315-9484131	GM12878	blood:	n/a	n/a
23	REST	chr11:9481019-9483943	H1-neurons	neurons:	n/a	chr11:9482673-9482686 chr11:9482938-9482951 chr11:9483091-9483104 chr11:9483077-9483090
24	RFX5	chr11:9481392-9483797	Hela-S3	cervix:	n/a	n/a
25	MAZ	chr11:9481298-9484039	IMR90	lung:	n/a	n/a
26	PML	chr11:9480975-9483622	K562	blood:	n/a	n/a
27	POLR2A	chr11:9479740-9484253	SK-N-MC	brain:	n/a	n/a
28	MAFK	chr11:9483417-9483718	HepG2	liver:	n/a	n/a
29	MTA3	chr11:9482719-9483657	GM12878	blood:	n/a	n/a
30	GATA3	chr11:9483312-9483701	SH-SY5Y	brain:	n/a	chr11:9483650-9483666
31	POLR2A	chr11:9480911-9484146	Raji	blood:	n/a	n/a
32	MAZ	chr11:9481295-9483622	K562	blood:	n/a	n/a
33	POLR2A	chr11:9483326-9483666	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr11:9480446-9484317	GM12892	blood:	n/a	n/a
35	POLR2A	chr11:9480935-9483857	U87	brain:	n/a	n/a
36	POLR2A	chr11:9481058-9483921	IMR90	lung:	n/a	n/a
37	POLR2A	chr11:9480731-9483814	GM12878	blood:	n/a	n/a
38	HCFC1	chr11:9481035-9483960	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr11:9481043-9483674	PBDE	blood:	n/a	n/a
40	POLR2A	chr11:9479623-9484236	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr11:9480933-9483774	K562	blood:	n/a	n/a
42	IRF1	chr11:9481990-9483564	K562	blood:	n/a	chr11:9482460-9482472
43	STAT3	chr11:9483320-9483533	GM12878	blood:	n/a	n/a
44	POLR2A	chr11:9479551-9483940	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr11:9479688-9485037	PANC-1	pancreas:	n/a	n/a
46	BCLAF1	chr11:9481246-9483878	GM12878	blood:	n/a	chr11:9482832-9482841 chr11:9482736-9482745 chr11:9482687-9482696 chr11:9482239-9482252 chr11:9482685-9482698 chr11:9482464-9482473
47	POLR2A	chr11:9483480-9483517	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr11:9481011-9483780	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr11:9483353-9483650	H1-hESC	embryonic stem cell:	n/a	n/a
50	USF2	chr11:9483126-9483590	Hela-S3	cervix:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:9481508..9485106-chr11:9595203..9601095,6	MCF-7	breast:
2	chr11:9482938..9483855-chr12:125398793..125399507,2	Hela-S3	cervix:
3	chr11:9227494..9229881-chr11:9482227..9483923,2	K562	blood:
4	chr11:9480226..9484903-chr11:9591788..9598525,12	MCF-7	breast:
5	chr11:8709096..8712017-chr11:9482712..9485056,2	K562	blood:
6	chr11:9333668..9337804-chr11:9478729..9484496,11	K562	blood:
7	chr11:9481080..9484532-chr11:9545856..9548015,3	MCF-7	breast:
8	chr11:9478618..9485582-chr11:9593299..9599536,13	K562	blood:
9	chr11:9285399..9287969-chr11:9480073..9484247,5	MCF-7	breast:
10	chr11:9481642..9483596-chr11:9779160..9782132,2	K562	blood:
11	chr11:9284942..9289829-chr11:9481407..9484206,5	MCF-7	breast:
12	chr11:9429811..9433973-chr11:9481355..9484368,4	MCF-7	breast:
13	chr11:9482164..9483690-chr11:9598599..9601195,2	MCF-7	breast:
14	chr11:9483118..9484824-chr11:9600066..9602856,2	K562	blood:
15	chr11:9405101..9410331-chr11:9478772..9485340,14	K562	blood:
16	chr11:9479692..9486524-chr11:9491765..9498081,14	K562	blood:
17	chr11:9334187..9337944-chr11:9481178..9484496,6	K562	blood:
18	chr11:9479099..9485582-chr11:9593306..9599058,18	K562	blood:
19	chr11:9403958..9411793-chr11:9477944..9485616,22	K562	blood:
20	chr11:9481460..9483596-chr11:9780067..9782132,2	K562	blood:
21	chr11:9422398..9424757-chr11:9482761..9485642,2	MCF-7	breast:
22	chr11:9452725..9455212-chr11:9482880..9484498,2	K562	blood:
23	chr11:9164859..9166403-chr11:9483116..9485555,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268403	TF binding region
ZNF143	TF binding region
ENSG00000205339	Chromatin interaction
ENSG00000243869	Chromatin interaction
ENSG00000254397	Chromatin interaction
ENSG00000184014	Chromatin interaction
ENSG00000166483	Chromatin interaction
ENSG00000150991	Chromatin interaction
ENSG00000166471	Chromatin interaction
ENSG00000238387	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000245522	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000246273	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1020621	0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1020622	0.89[ASN][1000 genomes]
rs10770028	0.95[JPT][hapmap]
rs10770032	0.95[JPT][hapmap]
rs10770033	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10770034	0.93[ASN][1000 genomes]
rs10770037	0.89[CEU][hapmap];0.87[CHD][hapmap];1.00[MEX][hapmap]
rs10840228	0.95[JPT][hapmap]
rs10840234	0.89[JPT][hapmap]
rs10840235	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10840236	0.82[ASN][1000 genomes]
rs10840237	0.87[ASN][1000 genomes]
rs10840238	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10840244	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10840245	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10840247	0.95[ASN][1000 genomes]
rs10840249	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840253	0.81[JPT][hapmap]
rs11042328	0.95[JPT][hapmap]
rs11042329	0.85[JPT][hapmap]
rs11042348	0.86[ASN][1000 genomes]
rs11042349	0.83[ASN][1000 genomes]
rs11042350	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11042353	0.89[ASN][1000 genomes]
rs11042355	0.89[ASN][1000 genomes]
rs11042356	0.89[ASN][1000 genomes]
rs11042366	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11042374	0.94[ASN][1000 genomes]
rs11042377	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11042393	0.88[ASN][1000 genomes]
rs11042395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11601316	0.87[ASN][1000 genomes]
rs11826606	0.83[ASN][1000 genomes]
rs12225755	0.83[ASN][1000 genomes]
rs12271897	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12282176	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12296039	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12792161	0.95[ASN][1000 genomes]
rs12795344	0.95[JPT][hapmap]
rs12797567	0.86[ASN][1000 genomes]
rs12800802	0.88[ASN][1000 genomes]
rs12806418	0.95[ASN][1000 genomes]
rs1377667	0.92[ASN][1000 genomes]
rs1470895	0.89[ASN][1000 genomes]
rs1470896	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1543	0.92[ASN][1000 genomes]
rs1968717	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278900	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs2290423	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290424	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs2290425	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs35781320	0.87[ASN][1000 genomes]
rs3763873	0.96[CEU][hapmap];0.89[GIH][hapmap]
rs3763874	0.87[CHD][hapmap];0.80[MEX][hapmap]
rs3763877	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41369549	0.95[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs4625466	0.90[JPT][hapmap]
rs4810	0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs4910048	0.86[GIH][hapmap]
rs4910053	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4910468	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6486307	0.95[JPT][hapmap]
rs6486359	0.89[ASN][1000 genomes]
rs6486361	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6486394	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs67548305	0.89[ASN][1000 genomes]
rs7102473	0.96[ASN][1000 genomes]
rs7104568	0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs7114824	0.81[ASN][1000 genomes]
rs7122252	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7122499	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs723297	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs727405	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729313	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7395411	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7483667	0.93[ASN][1000 genomes]
rs7926589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7927350	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7928945	0.84[AMR][1000 genomes]
rs7933621	0.96[ASN][1000 genomes]
rs7939724	0.89[CEU][hapmap];0.87[CHD][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs7944578	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7949973	0.89[ASN][1000 genomes]
rs8785	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9667574	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs972594	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv1039537	chr11:9455387-9535970	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10840243	SNORA23	cis	parietal	SCAN
rs10840243	IPO7	Cis_1M	lymphoblastoid	RTeQTL
rs10840243	SNORA23	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9480600-9483800	Active TSS	Placenta	Placenta
2	chr11:9480600-9484000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr11:9480800-9483600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:9480800-9483600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:9480800-9483600	Active TSS	Esophagus	oesophagus
6	chr11:9480800-9483600	Active TSS	Pancreas	Pancrea
7	chr11:9480800-9483800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:9480800-9483800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr11:9480800-9483800	Active TSS	GM12878-XiMat	blood
10	chr11:9480800-9484000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:9480800-9484000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:9480800-9484000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr11:9480800-9484000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:9480800-9484000	Active TSS	Fetal Brain Female	brain
15	chr11:9480800-9484000	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr11:9480800-9484200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr11:9480800-9484200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr11:9480800-9484200	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr11:9480800-9484200	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr11:9480800-9484200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:9480800-9484200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:9480800-9484200	Active TSS	HSMM	muscle
23	chr11:9481000-9483600	Active TSS	Liver	Liver
24	chr11:9481000-9483600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr11:9481000-9483600	Active TSS	Fetal Stomach	stomach
26	chr11:9481000-9483600	Active TSS	Left Ventricle	heart
27	chr11:9481000-9483600	Active TSS	NHDF-Ad	bronchial
28	chr11:9481000-9483800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr11:9481000-9483800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:9481000-9483800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:9481000-9483800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:9481000-9483800	Active TSS	Aorta	Aorta
33	chr11:9481000-9483800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr11:9481000-9483800	Active TSS	Fetal Intestine Large	intestine
35	chr11:9481000-9483800	Active TSS	Fetal Intestine Small	intestine
36	chr11:9481000-9483800	Active TSS	K562	blood
37	chr11:9481000-9484000	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr11:9481000-9484000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:9481000-9484000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:9481000-9484000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr11:9481000-9484000	Active TSS	Psoas Muscle	Psoas
42	chr11:9481000-9484000	Active TSS	Right Ventricle	heart
43	chr11:9481000-9484000	Active TSS	HSMMtube	muscle
44	chr11:9481000-9484000	Active TSS	NHLF	lung
45	chr11:9481000-9484200	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr11:9481000-9484600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:9481200-9483600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:9481200-9483600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr11:9481200-9483600	Active TSS	Brain Hippocampus Middle	brain
50	chr11:9481200-9483600	Active TSS	Colon Smooth Muscle	Colon

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