Variant report

Variant	rs7930105
Chromosome Location	chr11:33794984-33794985
allele	C/T
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	SIN3AK20	chr11:33794936-33795228	HepG2	liver:	n/a	n/a
2	SIN3AK20	chr11:33794923-33795337	PANC-1	pancreas:	n/a	n/a
3	MXI1	chr11:33794764-33797035	SK-N-SH	brain:	n/a	chr11:33795490-33795499
4	HCFC1	chr11:33794953-33797412	Hela-S3	cervix:	n/a	n/a
5	SIN3AK20	chr11:33794971-33795232	PFSK-1	brain:	n/a	n/a
6	MAX	chr11:33794974-33795226	K562	blood:	n/a	n/a
7	CTCF	chr11:33794980-33795130	A549	lung:	n/a	n/a
8	MXI1	chr11:33794939-33795328	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr11:33794957-33796345	GM12878	blood:	n/a	chr11:33796033-33796053
10	MAX	chr11:33794828-33796614	A549	lung:	n/a	chr11:33796160-33796170 chr11:33795877-33795887
11	MAX	chr11:33794910-33795341	SK-N-SH	brain:	n/a	n/a
12	SIN3AK20	chr11:33794983-33795469	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr11:33794965-33795344	GM12878	blood:	n/a	n/a
14	MAZ	chr11:33794961-33796438	GM12878	blood:	n/a	chr11:33796160-33796170 chr11:33795877-33795887
15	MAX	chr11:33794968-33795267	NB4	blood:	n/a	n/a
16	SIN3AK20	chr11:33794961-33795458	PFSK-1	brain:	n/a	n/a
17	ELK1	chr11:33794975-33795377	GM12878	blood:	n/a	chr11:33795318-33795327 chr11:33795318-33795327
18	SIN3AK20	chr11:33794946-33795267	A549	lung:	n/a	n/a
19	MAX	chr11:33794970-33795474	GM12878	blood:	n/a	n/a
20	YY1	chr11:33794978-33796333	GM12892	blood:	n/a	chr11:33796033-33796053
21	CTCF	chr11:33794960-33795110	GM12873	blood:	n/a	n/a
22	ZNF143	chr11:33794983-33795477	GM12878	blood:	n/a	n/a
23	GATA1	chr11:33794047-33795711	PBDE	blood:	n/a	chr11:33794371-33794392 chr11:33795221-33795233 chr11:33795219-33795235 chr11:33795223-33795232 chr11:33794534-33794544 chr11:33795221-33795234 chr11:33794367-33794384
24	MXI1	chr11:33794381-33795885	IMR90	lung:	n/a	chr11:33795490-33795499
25	SIN3A	chr11:33794966-33796691	H1-hESC	embryonic stem cell:	n/a	chr11:33795634-33795645 chr11:33796151-33796164 chr11:33795551-33795564
26	SIN3AK20	chr11:33794950-33796424	PANC-1	pancreas:	n/a	n/a
27	MAZ	chr11:33794894-33796593	IMR90	lung:	n/a	chr11:33796160-33796170 chr11:33795877-33795887
28	MXI1	chr11:33794861-33796611	GM12878	blood:	n/a	chr11:33795490-33795499
29	MXI1	chr11:33794930-33796588	HepG2	liver:	n/a	chr11:33795490-33795499
30	YY1	chr11:33794955-33796206	GM12878	blood:	n/a	chr11:33796033-33796053
31	SIN3A	chr11:33794900-33795413	GM12878	blood:	n/a	n/a
32	MAX	chr11:33794963-33795191	HepG2	liver:	n/a	n/a
33	SIN3AK20	chr11:33794975-33795282	A549	lung:	n/a	n/a
34	MAX	chr11:33794824-33795379	HepG2	liver:	n/a	n/a
35	MAX	chr11:33794979-33795161	K562	blood:	n/a	n/a
36	SIN3AK20	chr11:33794959-33795522	SK-N-SH	brain:	n/a	n/a
37	MAX	chr11:33794898-33795369	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:33757743..33759681-chr11:33794774..33797554,2	MCF-7	breast:
2	chr11:33756399..33761777-chr11:33794455..33799644,9	K562	blood:
3	chr11:33756496..33759717-chr11:33794342..33798618,4	K562	blood:
4	chr11:33720701..33723094-chr11:33794886..33797220,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255272	TF binding region
ENSG00000254508	TF binding region
FBXO3	TF binding region
ENSG00000085063	Chromatin interaction
ENSG00000205177	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10501127	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs10768030	0.85[CEU][hapmap]
rs11032377	0.95[CEU][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11032385	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11599935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11601836	0.83[EUR][1000 genomes]
rs11607434	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11607549	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608235	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12419271	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12420580	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1522086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17760306	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17760694	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767323	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2273121	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3181268	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181269	1.00[ASN][1000 genomes]
rs55933775	0.83[AMR][1000 genomes]
rs56026019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60691031	0.84[EUR][1000 genomes]
rs61887473	1.00[ASN][1000 genomes]
rs61887474	1.00[ASN][1000 genomes]
rs61887477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7480506	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7941387	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943459	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523356	chr11:33777334-33797408	Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7930105	CD59	cis	Artery Tibial	GTEx
rs7930105	CD59	Cis_1M	lymphoblastoid	RTeQTL
rs7930105	CD59	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33758800-33795000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:33759000-33795200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:33769600-33795000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:33779600-33795000	Weak transcription	Colonic Mucosa	Colon
5	chr11:33787600-33795000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr11:33790400-33795000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:33790800-33795000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:33792000-33795000	Weak transcription	HSMM	muscle
9	chr11:33792200-33795000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:33792200-33795000	Weak transcription	Aorta	Aorta
11	chr11:33792400-33795000	Weak transcription	Fetal Kidney	kidney
12	chr11:33792400-33795000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:33793000-33795000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:33793000-33795000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr11:33793000-33795000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr11:33793200-33795000	Enhancers	K562	blood
17	chr11:33793400-33795000	Enhancers	Colon Smooth Muscle	Colon
18	chr11:33793400-33795000	Enhancers	Pancreas	Pancrea
19	chr11:33793400-33795000	Enhancers	Right Ventricle	heart
20	chr11:33793600-33795000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:33793600-33795000	Enhancers	Fetal Heart	heart
22	chr11:33793600-33795000	Enhancers	Small Intestine	intestine
23	chr11:33793600-33795000	Enhancers	Spleen	Spleen
24	chr11:33794000-33795000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:33794000-33795000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr11:33794000-33795000	Enhancers	Primary B cells from peripheral blood	blood
27	chr11:33794000-33795000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:33794000-33795000	Enhancers	Esophagus	oesophagus
29	chr11:33794000-33795000	Enhancers	Placenta	Placenta
30	chr11:33794000-33795000	Enhancers	Left Ventricle	heart
31	chr11:33794000-33795000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr11:33794200-33795000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr11:33794200-33795000	Enhancers	Fetal Intestine Large	intestine
34	chr11:33794200-33795000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr11:33794200-33795000	Enhancers	Fetal Muscle Leg	muscle
36	chr11:33794200-33795000	Enhancers	Stomach Mucosa	stomach
37	chr11:33794200-33795200	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr11:33794200-33795200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr11:33794200-33795400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:33794200-33795400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr11:33794400-33795000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:33794400-33795000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:33794400-33795000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr11:33794400-33795000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr11:33794400-33795000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:33794400-33795000	Active TSS	Brain Germinal Matrix	brain
47	chr11:33794400-33795000	Enhancers	Fetal Brain Male	brain
48	chr11:33794400-33795000	Enhancers	Fetal Lung	lung
49	chr11:33794400-33795000	Enhancers	Lung	lung
50	chr11:33794400-33795000	Weak transcription	Ovary	ovary

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