Variant report

Variant	rs12001235
Chromosome Location	chr9:110046780-110046781
allele	A/C
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	MEF2C	chr9:110046768-110047256	GM12878	blood:	n/a	chr9:110047011-110047026 chr9:110047011-110047026 chr9:110047014-110047023 chr9:110047013-110047024 chr9:110047011-110047025 chr9:110047033-110047048
2	RELA	chr9:110044841-110047095	GM18505	blood:	n/a	n/a
3	MYBL2	chr9:110046696-110047540	HepG2	liver:	n/a	n/a
4	SIN3A	chr9:110045979-110047025	GM12878	blood:	n/a	n/a
5	SIN3AK20	chr9:110044700-110047350	MCF-7	breast:	n/a	n/a
6	BCLAF1	chr9:110046019-110047170	GM12878	blood:	n/a	chr9:110046044-110046057 chr9:110046065-110046074 chr9:110046054-110046067
7	ARID3A	chr9:110046153-110047491	HepG2	liver:	n/a	n/a
8	POLR2A	chr9:110044790-110046808	GM12878	blood:	n/a	n/a
9	CHD1	chr9:110044878-110048034	GM12878	blood:	n/a	chr9:110045625-110045635 chr9:110045424-110045434
10	NFIC	chr9:110046010-110046815	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:110044915-110047011	GM18951	blood:	n/a	n/a
12	CHD2	chr9:110046099-110046992	HepG2	liver:	n/a	n/a
13	TBP	chr9:110044972-110046805	H1-hESC	embryonic stem cell:	n/a	n/a
14	RELA	chr9:110044696-110047218	GM19099	blood:	n/a	n/a
15	POLR2A	chr9:110044741-110047105	HepG2	liver:	n/a	n/a
16	POLR2A	chr9:110044709-110047270	GM19099	blood:	n/a	n/a
17	HCFC1	chr9:110044730-110046903	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr9:110044257-110047284	HepG2	liver:	n/a	n/a
19	CHD1	chr9:110045534-110047746	H1-hESC	embryonic stem cell:	n/a	chr9:110045625-110045635
20	IRF1	chr9:110044798-110047893	K562	blood:	n/a	chr9:110045289-110045303 chr9:110045422-110045436
21	WRNIP1	chr9:110045848-110046821	GM12878	blood:	n/a	n/a
22	MXI1	chr9:110044978-110046798	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr9:110044892-110047240	GM18505	blood:	n/a	n/a
24	MXI1	chr9:110044294-110047293	IMR90	lung:	n/a	n/a
25	POLR2A	chr9:110044686-110048005	K562	blood:	n/a	n/a
26	TAF7	chr9:110044978-110046833	H1-hESC	embryonic stem cell:	n/a	n/a
27	RELA	chr9:110044973-110047131	GM10847	blood:	n/a	n/a
28	MEF2A	chr9:110046712-110047293	GM12878	blood:	n/a	chr9:110047011-110047026 chr9:110047014-110047023 chr9:110047013-110047024 chr9:110047011-110047025
29	SP1	chr9:110046025-110046786	H1-hESC	embryonic stem cell:	n/a	chr9:110046493-110046500 chr9:110046268-110046282 chr9:110046333-110046347 chr9:110046501-110046514
30	ZNF384	chr9:110046168-110046795	K562	blood:	n/a	n/a
31	HA-E2F1	chr9:110044802-110046813	MCF-7	breast:	n/a	chr9:110046048-110046057 chr9:110046450-110046465 chr9:110045460-110045469 chr9:110045426-110045435 chr9:110045375-110045384 chr9:110045458-110045467 chr9:110046552-110046564 chr9:110045488-110045497
32	GATA3	chr9:110046302-110047571	MCF-7	breast:	n/a	n/a
33	MAX	chr9:110046056-110046803	SK-N-SH	brain:	n/a	n/a
34	TAF1	chr9:110044783-110046794	H1-hESC	embryonic stem cell:	n/a	n/a
35	EP300	chr9:110046152-110047271	GM12878	blood:	n/a	chr9:110046772-110046786 chr9:110046765-110046779 chr9:110046764-110046778
36	HDAC2	chr9:110046076-110046789	MCF-7	breast:	n/a	chr9:110046768-110046782 chr9:110046764-110046778 chr9:110046282-110046290 chr9:110046762-110046776 chr9:110046759-110046773 chr9:110046430-110046444 chr9:110046766-110046780 chr9:110046427-110046441 chr9:110046772-110046786 chr9:110046773-110046787 chr9:110046760-110046774 chr9:110046763-110046777
37	IRF1	chr9:110046153-110047300	K562	blood:	n/a	n/a
38	UBTF	chr9:110045047-110046885	K562	blood:	n/a	n/a
39	MAX	chr9:110045018-110046803	K562	blood:	n/a	chr9:110045533-110045542
40	TCF12	chr9:110044766-110046830	A549	lung:	n/a	n/a
41	POLR2A	chr9:110044361-110047198	GM12891	blood:	n/a	n/a
42	TBL1XR1	chr9:110044490-110047918	GM12878	blood:	n/a	n/a
43	TBP	chr9:110046083-110047258	GM12878	blood:	n/a	n/a
44	NFATC1	chr9:110046059-110046805	GM12878	blood:	n/a	n/a
45	POLR2A	chr9:110044654-110046876	Hela-S3	cervix:	n/a	n/a
46	CHD2	chr9:110044671-110047242	GM12878	blood:	n/a	chr9:110045625-110045635 chr9:110045424-110045434
47	SIN3A	chr9:110044880-110046973	H1-hESC	embryonic stem cell:	n/a	chr9:110045855-110045866 chr9:110045867-110045876 chr9:110045128-110045137 chr9:110045853-110045866 chr9:110045722-110045735
48	POLR2A	chr9:110044427-110047255	GM12878	blood:	n/a	n/a
49	POLR2A	chr9:110044401-110046994	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr9:110044873-110047029	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:110044300..110048942-chr9:110067094..110074281,11	MCF-7	breast:
2	chr9:110045521..110048079-chr9:110251760..110253947,2	MCF-7	breast:
3	chr17:56738323..56740813-chr9:110045478..110047129,2	MCF-7	breast:

Variant related genes	Relation type
RAD23B	TF binding region
ENSG00000136826	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10978789	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10978793	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11573631	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11573652	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11573655	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11573700	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12001425	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12005299	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005522	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16912372	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17724694	1.00[EUR][1000 genomes]
rs56091145	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62567660	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567661	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567691	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567693	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567694	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567696	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62567704	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62567738	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73668766	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73668780	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7859324	0.84[EUR][1000 genomes];0.91[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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS 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
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110044200-110047600	Active TSS	Thymus	Thymus
2	chr9:110044200-110048200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr9:110044400-110047400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr9:110044400-110047600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:110044400-110047800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr9:110044400-110048000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr9:110044400-110048200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr9:110044400-110048200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr9:110044400-110048400	Active TSS	Fetal Kidney	kidney
10	chr9:110044400-110048800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr9:110044600-110047200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:110044600-110047800	Bivalent/Poised TSS	HepG2	liver
13	chr9:110044600-110048000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:110044600-110048200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr9:110044600-110048200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:110044600-110048200	Active TSS	A549	lung
17	chr9:110044600-110048400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:110044600-110048400	Active TSS	GM12878-XiMat	blood
19	chr9:110044600-110049000	Active TSS	Right Ventricle	heart
20	chr9:110044800-110046800	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr9:110044800-110046800	Active TSS	Esophagus	oesophagus
22	chr9:110044800-110046800	Active TSS	Gastric	stomach
23	chr9:110044800-110046800	Active TSS	Pancreas	Pancrea
24	chr9:110044800-110047000	Active TSS	Brain Anterior Caudate	brain
25	chr9:110044800-110047000	Active TSS	Small Intestine	intestine
26	chr9:110044800-110047200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:110044800-110047200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:110044800-110047200	Active TSS	Lung	lung
29	chr9:110044800-110047200	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr9:110044800-110047600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:110044800-110047600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:110044800-110047600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:110044800-110047600	Active TSS	Fetal Intestine Small	intestine
34	chr9:110044800-110047600	Active TSS	Stomach Mucosa	stomach
35	chr9:110044800-110047800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:110044800-110048000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:110044800-110048000	Active TSS	Aorta	Aorta
38	chr9:110044800-110048200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:110044800-110048200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:110044800-110048200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr9:110044800-110048200	Active TSS	Fetal Brain Female	brain
42	chr9:110044800-110048200	Active TSS	Fetal Lung	lung
43	chr9:110044800-110048400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:110044800-110048400	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr9:110044800-110048400	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr9:110044800-110048400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:110044800-110048400	Active TSS	Left Ventricle	heart
48	chr9:110044800-110048400	Active TSS	K562	blood
49	chr9:110044800-110048600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr9:110044800-110048600	Active TSS	Ovary	ovary

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