Variant report

Variant	rs11111980
Chromosome Location	chr12:104683024-104683025
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	BRCA1	chr12:104682117-104683361	Hela-S3	cervix:	n/a	n/a
2	RUNX3	chr12:104682396-104683047	GM12878	blood:	n/a	n/a
3	GATA3	chr12:104681970-104683989	A549	lung:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683191-104683199 chr12:104683216-104683229 chr12:104683841-104683851 chr12:104683193-104683210
4	POLR2A	chr12:104679566-104684466	PANC-1	pancreas:	n/a	n/a
5	CREB1	chr12:104682307-104683211	GM12878	blood:	n/a	n/a
6	WRNIP1	chr12:104682017-104683835	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:104680676-104684470	A549	lung:	n/a	n/a
8	POLR2A	chr12:104682049-104683470	K562	blood:	n/a	n/a
9	POLR2A	chr12:104679817-104683502	Hela-S3	cervix:	n/a	n/a
10	NRF1	chr12:104682603-104683110	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:104679670-104683975	HUVEC	blood vessel:	n/a	n/a
12	GATA3	chr12:104682287-104683460	SK-N-SH	brain:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683191-104683199 chr12:104683216-104683229 chr12:104683193-104683210
13	POLR2A	chr12:104682066-104683608	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr12:104682324-104683039	HL-60	blood:	n/a	n/a
15	SP1	chr12:104679158-104684055	A549	lung:	n/a	chr12:104682628-104682639 chr12:104683086-104683100
16	BCL3	chr12:104681838-104683936	A549	lung:	n/a	n/a
17	ELF1	chr12:104682944-104683455	A549	lung:	n/a	chr12:104683082-104683093
18	POLR2A	chr12:104679672-104683881	HepG2	liver:	n/a	n/a
19	MYC	chr12:104682273-104683291	NB4	blood:	n/a	n/a
20	MAX	chr12:104682079-104683156	ECC-1	luminal epithelium:	n/a	n/a
21	SIN3AK20	chr12:104681904-104684468	A549	lung:	n/a	n/a
22	TAL1	chr12:104682178-104683408	K562	blood:	n/a	n/a
23	YY1	chr12:104682283-104683034	H1-hESC	embryonic stem cell:	n/a	chr12:104682480-104682489
24	CREB1	chr12:104682256-104683048	HepG2	liver:	n/a	n/a
25	TCF12	chr12:104681919-104683573	A549	lung:	n/a	n/a
26	POLR2A	chr12:104682351-104683025	GM12891	blood:	n/a	n/a
27	POLR2A	chr12:104681942-104683905	HCT-116	colon:	n/a	n/a
28	BHLHE40	chr12:104682356-104683070	K562	blood:	n/a	n/a
29	GATA2	chr12:104682236-104683462	HUVEC	blood vessel:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683216-104683229 chr12:104683187-104683201 chr12:104683193-104683210
30	POLR2A	chr12:104682344-104683070	GM12891	blood:	n/a	n/a
31	TBL1XR1	chr12:104682030-104683344	K562	blood:	n/a	n/a
32	MXI1	chr12:104682098-104683086	K562	blood:	n/a	n/a
33	RFX5	chr12:104682046-104683396	Hela-S3	cervix:	n/a	n/a
34	EP300	chr12:104682229-104683091	GM12878	blood:	n/a	n/a
35	USF2	chr12:104682090-104683422	Hela-S3	cervix:	n/a	n/a
36	MTA3	chr12:104682048-104683494	GM12878	blood:	n/a	n/a
37	SIN3AK20	chr12:104682158-104683138	MCF-7	breast:	n/a	n/a
38	MYC	chr12:104682334-104683073	K562	blood:	n/a	n/a
39	MYC	chr12:104682379-104683357	K562	blood:	n/a	n/a
40	TAF7	chr12:104682146-104683026	H1-hESC	embryonic stem cell:	n/a	n/a
41	YY1	chr12:104682280-104683035	GM12878	blood:	n/a	chr12:104682480-104682489
42	MAX	chr12:104682423-104683139	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr12:104679831-104683884	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr12:104682357-104683249	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr12:104680251-104683962	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr12:104682430-104683138	H1-neurons	neurons:	n/a	n/a
47	CREB1	chr12:104682206-104683269	GM12878	blood:	n/a	n/a
48	MAX	chr12:104682297-104683043	SK-N-SH	brain:	n/a	n/a
49	GATA2	chr12:104682511-104683435	SH-SY5Y	brain:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683216-104683229 chr12:104683187-104683201 chr12:104683193-104683210
50	BACH1	chr12:104682189-104683077	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104682529..104684202-chr12:105629338..105630884,2	MCF-7	breast:
2	chr12:104348328..104351209-chr12:104680724..104683661,2	K562	blood:
3	chr12:104680142..104683904-chr12:104694272..104698636,5	MCF-7	breast:
4	chr12:104608375..104610840-chr12:104681920..104683609,3	MCF-7	breast:
5	chr12:104441752..104444274-chr12:104682358..104684016,2	K562	blood:
6	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:
7	chr12:104606650..104611349-chr12:104679680..104683932,8	K562	blood:
8	chr12:104643850..104647465-chr12:104679926..104684172,5	K562	blood:
9	chr12:104530429..104534144-chr12:104679811..104684673,6	MCF-7	breast:
10	chr12:104643349..104645898-chr12:104680595..104683102,2	K562	blood:
11	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:
12	chr12:104681662..104683943-chr12:104703194..104704714,2	MCF-7	breast:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000120820	Chromatin interaction
ENSG00000136044	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000255150	Chromatin interaction
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10778321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861185	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10861187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861190	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861193	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861195	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861196	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861198	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861199	1.00[CEU][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861208	0.89[ASN][1000 genomes]
rs11111938	0.85[JPT][hapmap]
rs11111940	0.86[JPT][hapmap]
rs11111945	0.81[JPT][hapmap]
rs11111979	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111981	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111984	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111987	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111995	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111996	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112006	0.92[ASN][1000 genomes]
rs11609469	0.89[ASN][1000 genomes]
rs12811618	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17202060	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17202520	0.92[ASN][1000 genomes]
rs4075411	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4445711	0.86[JPT][hapmap]
rs4595619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4601859	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964782	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964783	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964785	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5018287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132675	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297956	0.82[JPT][hapmap]
rs7298739	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310815	0.81[JPT][hapmap]
rs7488680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954970	0.85[JPT][hapmap]
rs7958262	0.87[JPT][hapmap]
rs7977410	0.94[ASN][1000 genomes]
rs7977553	0.92[ASN][1000 genomes]
rs7978051	0.92[ASN][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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11111980	EID3	cis	normal skin	skin_eQTL
rs11111980	EID3	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104680000-104683200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:104680000-104683400	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr12:104680000-104683600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:104680000-104683800	Active TSS	Aorta	Aorta
5	chr12:104680200-104683200	Active TSS	Brain Substantia Nigra	brain
6	chr12:104680400-104683200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:104680400-104683200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:104680400-104683200	Active TSS	Colon Smooth Muscle	Colon
9	chr12:104680400-104683200	Active TSS	Fetal Brain Female	brain
10	chr12:104680400-104683400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:104680400-104683400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:104680400-104683600	Active TSS	Brain Anterior Caudate	brain
13	chr12:104680400-104683600	Active TSS	Brain Cingulate Gyrus	brain
14	chr12:104680400-104683600	Active TSS	Brain Hippocampus Middle	brain
15	chr12:104680400-104683600	Active TSS	Fetal Kidney	kidney
16	chr12:104680400-104683600	Active TSS	Left Ventricle	heart
17	chr12:104680400-104683600	Active TSS	Ovary	ovary
18	chr12:104680400-104683600	Active TSS	Psoas Muscle	Psoas
19	chr12:104680400-104683600	Active TSS	Right Ventricle	heart
20	chr12:104680400-104683800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr12:104680400-104684000	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr12:104680400-104684000	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr12:104680400-104684000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr12:104680400-104684200	Active TSS	Right Atrium	heart
25	chr12:104680600-104683200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:104680600-104683200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:104680600-104683200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:104680600-104683200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:104680600-104683200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:104680600-104683200	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr12:104680600-104683200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:104680600-104683200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr12:104680600-104683200	Active TSS	Fetal Intestine Large	intestine
34	chr12:104680600-104683200	Active TSS	Stomach Mucosa	stomach
35	chr12:104680600-104683200	Active TSS	HMEC	breast
36	chr12:104680600-104683200	Active TSS	NH-A	brain
37	chr12:104680600-104683400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr12:104680600-104683400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr12:104680600-104683400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:104680600-104683400	Active TSS	Pancreas	Pancrea
41	chr12:104680600-104683600	Active TSS	H1 Cell Line	embryonic stem cell
42	chr12:104680600-104683600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:104680600-104683600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:104680600-104683600	Active TSS	Colonic Mucosa	Colon
45	chr12:104680600-104683600	Active TSS	Fetal Stomach	stomach
46	chr12:104680600-104683600	Active TSS	Lung	lung
47	chr12:104680600-104683600	Active TSS	Rectal Smooth Muscle	rectum
48	chr12:104680600-104683600	Active TSS	HSMM	muscle
49	chr12:104680600-104683600	Active TSS	NHDF-Ad	bronchial
50	chr12:104680600-104683800	Active TSS	H9 Cell Line	embryonic stem cell

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