Variant report

Variant	rs3935069
Chromosome Location	chr11:57078954-57078955
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	TAF1	chr11:57078547-57079162	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:57078273-57079154	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:57078483-57079026	GM12878	blood:	n/a	n/a
4	EP300	chr11:57078707-57079369	T-47D	breast:	n/a	chr11:57078862-57078878
5	TCF12	chr11:57077922-57079435	A549	lung:	n/a	chr11:57079185-57079195 chr11:57078862-57078872 chr11:57079130-57079140
6	HCFC1	chr11:57078939-57079055	K562	blood:	n/a	n/a
7	YY1	chr11:57078787-57079119	HCT-116	colon:	n/a	chr11:57078842-57078851 chr11:57078986-57079000 chr11:57079094-57079105
8	BCL3	chr11:57078155-57079251	A549	lung:	n/a	chr11:57079089-57079102 chr11:57078841-57078850 chr11:57078652-57078661
9	POLR2A	chr11:57078562-57079117	SK-N-SH	brain:	n/a	n/a
10	TAF1	chr11:57078806-57079079	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr11:57075726-57080675	PFSK-1	brain:	n/a	n/a
12	TCF12	chr11:57078739-57079294	H1-hESC	embryonic stem cell:	n/a	chr11:57079185-57079195 chr11:57078862-57078872 chr11:57079130-57079140
13	ZBTB7A	chr11:57078546-57079383	ECC-1	luminal epithelium:	n/a	chr11:57079140-57079147
14	POLR2A	chr11:57078696-57079153	ECC-1	luminal epithelium:	n/a	n/a
15	RCOR1	chr11:57078850-57079053	K562	blood:	n/a	n/a
16	POLR2A	chr11:57078448-57079116	K562	blood:	n/a	n/a
17	JUND	chr11:57078422-57079250	A549	lung:	n/a	chr11:57079015-57079025 chr11:57079090-57079099 chr11:57078701-57078713 chr11:57078704-57078715 chr11:57078702-57078713 chr11:57078703-57078711 chr11:57078701-57078712 chr11:57079016-57079024
18	CEBPD	chr11:57078815-57079261	HepG2	liver:	n/a	n/a
19	POLR2A	chr11:57078549-57079192	Gliobla	brain:	n/a	n/a
20	ZC3H11A	chr11:57078669-57079130	K562	blood:	n/a	n/a
21	POLR2A	chr11:57078188-57079275	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr11:57078440-57079614	SK-N-MC	brain:	n/a	n/a
23	JUND	chr11:57078841-57079203	H1-hESC	embryonic stem cell:	n/a	chr11:57079015-57079025 chr11:57079090-57079099 chr11:57079016-57079024
24	POLR2A	chr11:57078240-57079346	MCF10A-Er-Src	breast:	n/a	n/a
25	EP300	chr11:57078346-57079001	A549	lung:	n/a	chr11:57078862-57078878
26	JUND	chr11:57078587-57079167	H1-hESC	embryonic stem cell:	n/a	chr11:57079015-57079025 chr11:57079090-57079099 chr11:57078701-57078713 chr11:57078704-57078715 chr11:57078702-57078713 chr11:57078703-57078711 chr11:57078701-57078712 chr11:57079016-57079024
27	CHD2	chr11:57078345-57079036	HepG2	liver:	n/a	n/a
28	YY1	chr11:57078745-57079162	K562	blood:	n/a	chr11:57078842-57078851 chr11:57078986-57079000 chr11:57079094-57079105
29	PBX3	chr11:57078506-57079334	SK-N-SH	brain:	n/a	n/a
30	SIN3AK20	chr11:57078841-57079094	A549	lung:	n/a	n/a
31	ATF3	chr11:57078534-57079165	K562	blood:	n/a	chr11:57078842-57078851 chr11:57079089-57079098
32	MYC	chr11:57078865-57079412	NB4	blood:	n/a	n/a
33	ZBTB7A	chr11:57078313-57079413	ECC-1	luminal epithelium:	n/a	chr11:57079140-57079147
34	ELF1	chr11:57078858-57079363	GM12878	blood:	n/a	n/a
35	ZMIZ1	chr11:57078648-57079150	K562	blood:	n/a	n/a
36	POLR2A	chr11:57078292-57079534	MCF10A-Er-Src	breast:	n/a	n/a
37	E2F4	chr11:57078557-57079369	MCF10A-Er-Src	breast:	n/a	chr11:57078716-57078728 chr11:57078842-57078851
38	POLR2A	chr11:57078576-57079068	GM12878	blood:	n/a	n/a
39	CBX3	chr11:57078824-57079222	K562	blood:	n/a	n/a
40	POLR2A	chr11:57078537-57079348	ECC-1	luminal epithelium:	n/a	n/a
41	TBP	chr11:57078660-57079371	H1-hESC	embryonic stem cell:	n/a	n/a
42	NR3C1	chr11:57078504-57079138	A549	lung:	n/a	chr11:57078703-57078712
43	UBTF	chr11:57078594-57079048	K562	blood:	n/a	n/a
44	EP300	chr11:57078325-57079444	ECC-1	luminal epithelium:	n/a	chr11:57078862-57078878
45	POLR2A	chr11:57078040-57079129	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr11:57078680-57079105	MCF-7	breast:	n/a	n/a
47	FOS	chr11:57078515-57079272	MCF10A-Er-Src	breast:	n/a	chr11:57079015-57079025 chr11:57078701-57078712 chr11:57079090-57079099 chr11:57078701-57078713 chr11:57078704-57078715 chr11:57078702-57078713 chr11:57078703-57078711 chr11:57079016-57079024
48	SIN3AK20	chr11:57078785-57079063	K562	blood:	n/a	n/a
49	TAF1	chr11:57078757-57079177	ECC-1	luminal epithelium:	n/a	n/a
50	TCF12	chr11:57078418-57079384	SK-N-SH	brain:	n/a	chr11:57079185-57079195 chr11:57078862-57078872 chr11:57079130-57079140

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57078335..57079106-chr2:96810799..96811698,2	Hela-S3	cervix:
2	chr1:205781878..205782419-chr11:57078284..57079137,2	Hela-S3	cervix:

Variant related genes	Relation type
TNKS1BP1	TF binding region
ENSG00000133065	Chromatin interaction
ENSG00000158050	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10732882	0.82[ASN][1000 genomes]
rs10792083	0.90[ASN][1000 genomes]
rs10792085	0.91[ASN][1000 genomes]
rs10896596	0.91[ASN][1000 genomes]
rs10896601	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896602	0.91[ASN][1000 genomes]
rs10896609	0.80[ASN][1000 genomes]
rs11228971	0.91[ASN][1000 genomes]
rs11228988	0.90[ASN][1000 genomes]
rs11602501	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11604373	0.89[ASN][1000 genomes]
rs17573746	0.98[ASN][1000 genomes]
rs1939496	0.98[ASN][1000 genomes]
rs4939129	0.98[ASN][1000 genomes]
rs4939131	0.98[ASN][1000 genomes]
rs4939134	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5012051	0.84[EUR][1000 genomes]
rs55637147	0.82[ASN][1000 genomes]
rs7130020	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7928905	0.88[ASN][1000 genomes]
rs7931298	0.93[ASN][1000 genomes]
rs7936545	0.85[ASN][1000 genomes]
rs7943761	0.90[ASN][1000 genomes]
rs7943915	0.98[ASN][1000 genomes]
rs7948723	0.98[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	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv541048	chr11:57076815-57120781	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57067400-57079000	Weak transcription	Primary B cells from cord blood	blood
2	chr11:57068400-57081600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:57074400-57081800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:57075000-57080600	Genic enhancers	Spleen	Spleen
5	chr11:57076200-57080600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:57077600-57082200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:57077800-57079200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr11:57077800-57079600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:57077800-57080000	Genic enhancers	Brain Substantia Nigra	brain
10	chr11:57077800-57080000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
11	chr11:57078000-57079000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr11:57078000-57079000	Flanking Active TSS	Pancreas	Pancrea
13	chr11:57078000-57079200	Active TSS	Psoas Muscle	Psoas
14	chr11:57078000-57079400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:57078000-57079600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:57078000-57079800	Enhancers	Fetal Heart	heart
17	chr11:57078000-57080000	Genic enhancers	Brain Cingulate Gyrus	brain
18	chr11:57078000-57080600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
19	chr11:57078200-57079000	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:57078200-57079200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
21	chr11:57078200-57079400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr11:57078200-57079400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr11:57078200-57079400	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr11:57078200-57079400	Flanking Active TSS	Placenta	Placenta
25	chr11:57078200-57079600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:57078200-57079600	Flanking Active TSS	Colonic Mucosa	Colon
27	chr11:57078200-57079600	Enhancers	Fetal Brain Male	brain
28	chr11:57078200-57079600	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr11:57078400-57079000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:57078400-57079000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr11:57078400-57079000	Active TSS	Aorta	Aorta
32	chr11:57078400-57079000	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr11:57078400-57079000	Active TSS	Esophagus	oesophagus
34	chr11:57078400-57079000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr11:57078400-57079000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr11:57078400-57079000	Transcr. at gene 5' and 3'	Right Atrium	heart
37	chr11:57078400-57079000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr11:57078400-57079200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:57078400-57079400	Weak transcription	Fetal Kidney	kidney
40	chr11:57078400-57079400	Flanking Active TSS	Thymus	Thymus
41	chr11:57078400-57079400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr11:57078400-57079600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr11:57078400-57079600	Enhancers	Primary B cells from peripheral blood	blood
44	chr11:57078400-57079600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:57078400-57079600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:57078400-57079600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr11:57078400-57079600	Flanking Active TSS	Fetal Muscle Trunk	muscle
48	chr11:57078400-57079800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:57078600-57079000	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr11:57078600-57079000	Active TSS	H1 Cell Line	embryonic stem cell

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