Variant report

Variant	rs10840457
Chromosome Location	chr11:10675738-10675739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr11:10675682-10676132	A549	lung:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
2	SP1	chr11:10675687-10677428	HCT-116	colon:	n/a	n/a
3	YY1	chr11:10675625-10676184	GM12878	blood:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
4	RAD21	chr11:10675727-10676256	HepG2	liver:	n/a	chr11:10676007-10676026
5	CBX3	chr11:10675611-10676221	K562	blood:	n/a	n/a
6	RAD21	chr11:10675506-10676419	SK-N-SH	brain:	n/a	chr11:10676007-10676026 chr11:10676363-10676370
7	CTCF	chr11:10675307-10676475	A549	lung:	n/a	chr11:10676010-10676026 chr11:10676009-10676027 chr11:10676004-10676025
8	YY1	chr11:10675738-10676084	GM12891	blood:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
9	CTCF	chr11:10675547-10676820	SK-N-SH	brain:	n/a	chr11:10676010-10676026 chr11:10676009-10676027 chr11:10676004-10676025
10	SMC3	chr11:10675705-10676260	GM12878	blood:	n/a	chr11:10676011-10676025
11	YY1	chr11:10675668-10676163	GM12892	blood:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
12	YY1	chr11:10675683-10676097	SK-N-SH_RA	brain:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
13	TEAD4	chr11:10675727-10676197	K562	blood:	n/a	n/a
14	RAD21	chr11:10675659-10676300	MCF-7	breast:	n/a	chr11:10676007-10676026
15	RAD21	chr11:10675590-10676423	HCT-116	colon:	n/a	chr11:10676007-10676026 chr11:10676363-10676370
16	CUX1	chr11:10675696-10676067	K562	blood:	n/a	n/a
17	CTCF	chr11:10675640-10675790	HAc	cerebellar:	n/a	n/a
18	RAD21	chr11:10675532-10677194	HCT-116	colon:	n/a	chr11:10676007-10676026 chr11:10676363-10676370
19	CTCF	chr11:10675640-10676680	HCT-116	colon:	n/a	chr11:10676010-10676026 chr11:10676009-10676027 chr11:10676004-10676025
20	RAD21	chr11:10675722-10676231	H1-hESC	embryonic stem cell:	n/a	chr11:10676007-10676026
21	SMC3	chr11:10675423-10676487	SK-N-SH	brain:	n/a	chr11:10676011-10676025
22	YY1	chr11:10675584-10676232	H1-hESC	embryonic stem cell:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
23	RAD21	chr11:10675674-10676299	ECC-1	luminal epithelium:	n/a	chr11:10676007-10676026
24	YY1	chr11:10675728-10676100	ECC-1	luminal epithelium:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
25	YY1	chr11:10675603-10676181	GM12892	blood:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
26	CTCF	chr11:10675721-10676291	K562	blood:	n/a	chr11:10676010-10676026 chr11:10676009-10676027 chr11:10676004-10676025
27	RAD21	chr11:10675721-10676228	A549	lung:	n/a	chr11:10676007-10676026
28	ELK1	chr11:10675639-10675778	K562	blood:	n/a	n/a
29	SP1	chr11:10675697-10677347	HCT-116	colon:	n/a	n/a
30	YY1	chr11:10675664-10676134	HCT-116	colon:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
31	YY1	chr11:10675728-10676167	SK-N-SH_RA	brain:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
32	CTCF	chr11:10675620-10675770	SK-N-SH_RA	brain:	n/a	n/a
33	YY1	chr11:10675718-10676182	SK-N-SH	brain:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
34	RUNX3	chr11:10675717-10676155	GM12878	blood:	n/a	n/a
35	YY1	chr11:10675629-10676117	GM12878	blood:	n/a	chr11:10675942-10675964 chr11:10675941-10675953 chr11:10675939-10675959 chr11:10675940-10675959
36	RAD21	chr11:10675727-10676226	SK-N-SH_RA	brain:	n/a	chr11:10676007-10676026

No.	Distal block	Cell Line	Cell type
1	chr11:10584920..10587068-chr11:10674559..10677361,2	K562	blood:
2	chr11:10427811..10428324-chr11:10675560..10676361,2	MCF-7	breast:
3	chr11:10427762..10428619-chr11:10675503..10676394,3	K562	blood:
4	chr11:10675148..10677906-chr11:10678421..10681418,4	MCF-7	breast:
5	chr11:10645864..10646419-chr11:10675380..10676170,2	MCF-7	breast:
6	chr11:10535531..10536556-chr11:10675584..10676325,3	MCF-7	breast:
7	chr11:10322610..10325546-chr11:10673380..10676333,2	K562	blood:
8	chr11:10534042..10535923-chr11:10675097..10677538,2	MCF-7	breast:
9	chr11:10560102..10563921-chr11:10672313..10677222,4	MCF-7	breast:
10	chr11:10674925..10678334-chr11:10679453..10682484,4	MCF-7	breast:
11	chr11:10675716..10676486-chr11:10756936..10757598,2	K562	blood:
12	chr11:10645746..10646712-chr11:10675224..10676417,4	K562	blood:

Variant related genes	Relation type
MRVI1	TF binding region
ENSG00000177112	Chromatin interaction
ENSG00000254554	Chromatin interaction
ENSG00000110315	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1035691	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10840453	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042902	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs11042906	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603178	1.00[JPT][hapmap]
rs1462940	1.00[JPT][hapmap]
rs1544861	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16908001	1.00[JPT][hapmap]
rs16927077	1.00[JPT][hapmap]
rs17318955	1.00[JPT][hapmap]
rs17403439	1.00[JPT][hapmap]
rs17403460	1.00[JPT][hapmap]
rs17403795	1.00[JPT][hapmap]
rs17403942	1.00[JPT][hapmap]
rs17403977	1.00[JPT][hapmap]
rs1863243	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863244	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1979367	1.00[JPT][hapmap]
rs2052690	0.90[AMR][1000 genomes]
rs2052691	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052692	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2098839	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4025	1.00[JPT][hapmap]
rs41464450	1.00[JPT][hapmap]
rs4442541	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4909945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910160	1.00[JPT][hapmap]
rs4910165	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484437	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936275	0.84[AMR][1000 genomes]
rs7940646	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881869	1.00[JPT][hapmap]
rs903822	1.00[JPT][hapmap]
rs903823	1.00[JPT][hapmap]

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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10840457	STK33	cis	parietal	SCAN
rs10840457	USP47	cis	cerebellum	SCAN
rs10840457	SPON1	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10646000-10679000	Weak transcription	Fetal Lung	lung
2	chr11:10646200-10679200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:10650400-10678600	Weak transcription	Right Ventricle	heart
4	chr11:10658800-10676600	Enhancers	Primary B cells from peripheral blood	blood
5	chr11:10664200-10678800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:10669600-10676800	Weak transcription	Fetal Intestine Large	intestine
7	chr11:10670800-10676400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:10671000-10676200	Weak transcription	A549	lung
9	chr11:10671400-10676000	Enhancers	Brain Anterior Caudate	brain
10	chr11:10671400-10676200	Enhancers	Brain Hippocampus Middle	brain
11	chr11:10671400-10677000	Weak transcription	Fetal Intestine Small	intestine
12	chr11:10672000-10679200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr11:10673000-10682200	Enhancers	Placenta	Placenta
14	chr11:10673200-10675800	Enhancers	Lung	lung
15	chr11:10673200-10676200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:10673200-10676800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr11:10673200-10677800	Enhancers	Colon Smooth Muscle	Colon
18	chr11:10673400-10676000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:10673400-10676600	Enhancers	Spleen	Spleen
20	chr11:10673400-10679200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr11:10673400-10682800	Enhancers	Ovary	ovary
22	chr11:10673600-10678400	Weak transcription	Left Ventricle	heart
23	chr11:10673600-10678400	Weak transcription	Right Atrium	heart
24	chr11:10673800-10676200	Weak transcription	Osteobl	bone
25	chr11:10673800-10678800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:10673800-10679200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:10673800-10681400	Weak transcription	Pancreas	Pancrea
28	chr11:10674000-10675800	Enhancers	Esophagus	oesophagus
29	chr11:10674000-10676000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:10674000-10676200	Enhancers	Brain Substantia Nigra	brain
31	chr11:10674000-10676400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:10674000-10676600	Weak transcription	NH-A	brain
33	chr11:10674000-10677200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:10674000-10677400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:10674000-10681400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:10674200-10676600	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr11:10674200-10681800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr11:10674400-10675800	Enhancers	Brain Angular Gyrus	brain
39	chr11:10674400-10675800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr11:10674400-10676200	Enhancers	Brain Cingulate Gyrus	brain
41	chr11:10674400-10678000	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr11:10674400-10681400	Enhancers	Fetal Muscle Leg	muscle
43	chr11:10674400-10681800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr11:10674600-10676000	Weak transcription	NHDF-Ad	bronchial
45	chr11:10674600-10678400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:10674600-10678400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:10674600-10689600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr11:10674800-10677000	Weak transcription	Colonic Mucosa	Colon
49	chr11:10674800-10678800	Enhancers	Rectal Smooth Muscle	rectum
50	chr11:10675000-10676000	Weak transcription	NHLF	lung

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