Variant report

Variant	rs11050079
Chromosome Location	chr12:29301234-29301235
allele	C/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	POLR2A	chr12:29301084-29302716	HUVEC	blood vessel:	n/a	n/a
2	ELF1	chr12:29300940-29301436	MCF-7	breast:	n/a	chr12:29301162-29301173
3	POLR2A	chr12:29301057-29303694	NB4	blood:	n/a	n/a
4	MYC	chr12:29301019-29303692	NB4	blood:	n/a	chr12:29302778-29302787
5	USF1	chr12:29301094-29301339	K562	blood:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199
6	MYC	chr12:29301029-29301391	K562	blood:	n/a	n/a
7	GTF2F1	chr12:29301193-29301349	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr12:29301000-29303723	NB4	blood:	n/a	chr12:29302778-29302787
9	USF1	chr12:29301066-29301263	SK-N-SH_RA	brain:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199
10	TCF12	chr12:29301168-29301465	H1-hESC	embryonic stem cell:	n/a	chr12:29301339-29301346
11	POLR2A	chr12:29301120-29303297	GM18951	blood:	n/a	n/a
12	BHLHE40	chr12:29301015-29301680	K562	blood:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199
13	USF1	chr12:29301068-29301365	H1-hESC	embryonic stem cell:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199
14	POLR2A	chr12:29300990-29303986	H1-hESC	embryonic stem cell:	n/a	n/a
15	BHLHE40	chr12:29301107-29301264	A549	lung:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199
16	POLR2A	chr12:29301007-29302822	HUVEC	blood vessel:	n/a	n/a
17	MAX	chr12:29301071-29301238	K562	blood:	n/a	n/a
18	CHD1	chr12:29301105-29301850	H1-hESC	embryonic stem cell:	n/a	chr12:29301793-29301800
19	MAX	chr12:29301032-29301607	H1-hESC	embryonic stem cell:	n/a	n/a
20	ELF1	chr12:29300861-29301565	HCT-116	colon:	n/a	chr12:29301162-29301173
21	ELF1	chr12:29301032-29301394	K562	blood:	n/a	chr12:29301162-29301173
22	USF1	chr12:29301090-29301308	SK-N-SH_RA	brain:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199
23	POLR2A	chr12:29300953-29302719	U87	brain:	n/a	n/a
24	MAX	chr12:29301050-29301262	H1-hESC	embryonic stem cell:	n/a	n/a
25	USF1	chr12:29301050-29301374	SK-N-SH	brain:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199
26	SIN3A	chr12:29301118-29302684	H1-hESC	embryonic stem cell:	n/a	chr12:29301977-29301986
27	MAX	chr12:29301081-29301264	K562	blood:	n/a	n/a
28	POLR2A	chr12:29301106-29303469	HL-60	blood:	n/a	n/a
29	POLR2A	chr12:29301222-29303487	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZMIZ1	chr12:29301151-29301309	K562	blood:	n/a	n/a
31	POLR2A	chr12:29301171-29302792	GM12891	blood:	n/a	n/a
32	ELF1	chr12:29300946-29301476	SK-N-SH	brain:	n/a	chr12:29301162-29301173
33	POLR2A	chr12:29301171-29303406	GM19099	blood:	n/a	n/a
34	MYC	chr12:29301086-29302952	K562	blood:	n/a	chr12:29302778-29302787
35	POLR2A	chr12:29301056-29301696	H1-neurons	neurons:	n/a	n/a
36	POLR2A	chr12:29300776-29302753	HUVEC	blood vessel:	n/a	n/a
37	ELF1	chr12:29300912-29301443	MCF-7	breast:	n/a	chr12:29301162-29301173
38	MXI1	chr12:29300813-29302759	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr12:29301004-29301329	HCT-116	colon:	n/a	n/a
40	USF1	chr12:29300955-29301437	HCT-116	colon:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199
41	POLR2A	chr12:29301182-29303050	K562	blood:	n/a	n/a
42	POLR2A	chr12:29300982-29302673	U87	brain:	n/a	n/a
43	ELF1	chr12:29300795-29301574	HCT-116	colon:	n/a	chr12:29301162-29301173
44	USF1	chr12:29301080-29301290	H1-hESC	embryonic stem cell:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199
45	RCOR1	chr12:29301042-29301689	K562	blood:	n/a	n/a
46	BHLHE40	chr12:29301082-29301377	GM12878	blood:	n/a	chr12:29301191-29301200 chr12:29301190-29301199 chr12:29301190-29301199

Variant related genes	Relation type
FAR2	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10492385	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10771493	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050088	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050117	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12371983	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2196488	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4414260	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4931157	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6487782	0.80[EUR][1000 genomes]
rs7296314	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7969731	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv819469	chr12:29285461-29303486	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3337951	chr12:29288734-29303032	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11050079	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29300200-29301600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:29300600-29301600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr12:29300600-29301600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:29300600-29301800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr12:29300600-29303200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:29300800-29301400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
7	chr12:29300800-29301400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:29301000-29301400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:29301000-29301400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:29301000-29301400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr12:29301000-29301400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:29301000-29301400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr12:29301000-29301400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:29301000-29301400	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr12:29301000-29301400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr12:29301000-29301400	Enhancers	Stomach Mucosa	stomach
17	chr12:29301000-29301400	Flanking Active TSS	NHDF-Ad	bronchial
18	chr12:29301000-29301600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr12:29301000-29301600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr12:29301000-29301600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr12:29301000-29301600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:29301000-29301600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr12:29301000-29301600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:29301000-29301600	Flanking Active TSS	Dnd41	blood
25	chr12:29301000-29301600	Flanking Active TSS	GM12878-XiMat	blood
26	chr12:29301000-29301600	Flanking Active TSS	HMEC	breast
27	chr12:29301000-29301600	Flanking Active TSS	HUVEC	blood vessel
28	chr12:29301000-29301600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr12:29301000-29301800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:29301000-29301800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr12:29301000-29301800	Flanking Active TSS	Fetal Muscle Trunk	muscle
32	chr12:29301000-29301800	Flanking Active TSS	NHEK	skin
33	chr12:29301000-29302000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr12:29301000-29302600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:29301000-29302600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:29301000-29303000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:29301000-29303000	Active TSS	Brain Substantia Nigra	brain
38	chr12:29301000-29303200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr12:29301000-29303200	Active TSS	Psoas Muscle	Psoas
40	chr12:29301000-29303400	Active TSS	Fetal Kidney	kidney
41	chr12:29301000-29303400	Active TSS	Stomach Smooth Muscle	stomach
42	chr12:29301000-29303600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:29301000-29304200	Active TSS	Brain Cingulate Gyrus	brain
44	chr12:29301200-29301400	Active TSS	H1 Cell Line	embryonic stem cell
45	chr12:29301200-29301400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:29301200-29301400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:29301200-29301400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:29301200-29301400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:29301200-29301400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:29301200-29301400	Flanking Active TSS	Duodenum Mucosa	Duodenum

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