Variant report

Variant	rs1411413
Chromosome Location	chr9:72375053-72375054
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	EP300	chr9:72374809-72375166	GM12878	blood:	n/a	chr9:72374996-72375003
2	POLR2A	chr9:72374236-72375777	MCF10A-Er-Src	breast:	n/a	n/a
3	TAF1	chr9:72374642-72375238	GM12891	blood:	n/a	n/a
4	TAF1	chr9:72374349-72375134	H1-neurons	neurons:	n/a	n/a
5	NFIC	chr9:72374840-72375273	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:72374533-72375311	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr9:72374307-72375363	NB4	blood:	n/a	chr9:72374718-72374728
8	ZNF263	chr9:72374014-72375103	HEK293-T-REx	kidney:	n/a	chr9:72374641-72374650
9	TAF1	chr9:72374206-72375289	GM12878	blood:	n/a	n/a
10	CHD2	chr9:72374245-72375314	GM12878	blood:	n/a	n/a
11	PBX3	chr9:72374221-72375320	SK-N-SH	brain:	n/a	n/a
12	HEY1	chr9:72374368-72375300	K562	blood:	n/a	chr9:72374896-72374911 chr9:72374712-72374727
13	POLR2A	chr9:72373418-72375715	Hela-S3	cervix:	n/a	n/a
14	ELF1	chr9:72374650-72375086	K562	blood:	n/a	chr9:72374883-72374892 chr9:72374996-72375005 chr9:72374712-72374724 chr9:72374995-72375006 chr9:72375072-72375081 chr9:72374750-72374762 chr9:72374749-72374758 chr9:72374995-72375006 chr9:72374994-72375007
15	SIN3A	chr9:72373980-72375230	GM12878	blood:	n/a	chr9:72374595-72374608
16	TAF1	chr9:72374343-72375199	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr9:72375040-72375190	HPAF	blood vessel:	n/a	n/a
18	ELF1	chr9:72374541-72375220	MCF-7	breast:	n/a	chr9:72374883-72374892 chr9:72374996-72375005 chr9:72374712-72374724 chr9:72374995-72375006 chr9:72375072-72375081 chr9:72374750-72374762 chr9:72374749-72374758 chr9:72374995-72375006 chr9:72374994-72375007
19	TAF7	chr9:72374379-72375266	H1-hESC	embryonic stem cell:	n/a	n/a
20	MYC	chr9:72374996-72375078	HepG2	liver:	n/a	n/a
21	POLR2A	chr9:72374063-72375534	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr9:72374297-72375257	HepG2	liver:	n/a	chr9:72374595-72374608
23	POLR2A	chr9:72374258-72375413	GM12892	blood:	n/a	n/a
24	YY1	chr9:72374315-72375087	ECC-1	luminal epithelium:	n/a	chr9:72374713-72374722 chr9:72374743-72374757 chr9:72374711-72374725 chr9:72374749-72374758 chr9:72374682-72374691 chr9:72374717-72374731 chr9:72374846-72374858 chr9:72374716-72374725
25	TBP	chr9:72374312-72375234	HepG2	liver:	n/a	n/a
26	POU2F2	chr9:72374931-72375211	GM12878	blood:	n/a	n/a
27	MAZ	chr9:72374420-72375246	K562	blood:	n/a	chr9:72374718-72374728
28	POLR2A	chr9:72374136-72375375	GM12878	blood:	n/a	n/a
29	POLR2A	chr9:72374304-72375338	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr9:72373830-72375462	Raji	blood:	n/a	n/a
31	YY1	chr9:72374414-72375189	GM12878	blood:	n/a	chr9:72374713-72374722 chr9:72374743-72374757 chr9:72374711-72374725 chr9:72374749-72374758 chr9:72374682-72374691 chr9:72374717-72374731 chr9:72374846-72374858 chr9:72374716-72374725
32	CEBPB	chr9:72374270-72375149	Hela-S3	cervix:	n/a	chr9:72375125-72375137
33	PAX5	chr9:72374707-72375157	GM12878	blood:	n/a	n/a
34	MAX	chr9:72374435-72375247	K562	blood:	n/a	chr9:72374718-72374728
35	RCOR1	chr9:72374340-72375392	GM12878	blood:	n/a	n/a
36	CTCF	chr9:72374833-72375154	Spleen_OC	spleen:	n/a	n/a
37	MAX	chr9:72373936-72375291	Hela-S3	cervix:	n/a	chr9:72374718-72374728
38	POLR2A	chr9:72374638-72375477	K562	blood:	n/a	n/a
39	FOXM1	chr9:72374453-72375321	GM12878	blood:	n/a	n/a
40	NFYA	chr9:72374854-72375327	Hela-S3	cervix:	n/a	n/a
41	GABPA	chr9:72374293-72375296	HL-60	blood:	n/a	chr9:72374713-72374722 chr9:72374719-72374728
42	EP300	chr9:72374730-72375291	HepG2	liver:	n/a	chr9:72375186-72375199 chr9:72374996-72375003
43	CTCF	chr9:72374980-72375130	HMF	breast:	n/a	n/a
44	E2F6	chr9:72374761-72375078	K562	blood:	n/a	n/a
45	TCF12	chr9:72374714-72375183	GM12878	blood:	n/a	n/a
46	E2F6	chr9:72374592-72375256	A549	lung:	n/a	chr9:72374719-72374728 chr9:72374713-72374722 chr9:72374682-72374691
47	POLR2A	chr9:72374387-72375650	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr9:72374154-72375464	SK-N-SH	brain:	n/a	n/a
49	SIN3AK20	chr9:72374463-72375275	PANC-1	pancreas:	n/a	n/a
50	SIN3AK20	chr9:72374414-72375443	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:72375036..72375536-chr9:73035083..73036042,2	Hela-S3	cervix:
2	chr9:72375011..72377307-chr9:72377548..72379098,2	K562	blood:
3	chr9:72286195..72289118-chr9:72373474..72376010,3	MCF-7	breast:
4	chr1:156698163..156698747-chr9:72374771..72375332,2	Hela-S3	cervix:
5	chr9:72287056..72289421-chr9:72373634..72375235,2	MCF-7	breast:
6	chr9:72375017..72376522-chr9:72378625..72381142,2	MCF-7	breast:
7	chr22:19434749..19435514-chr9:72374574..72375312,2	Hela-S3	cervix:
8	chr9:72373387..72376208-chr9:72873924..72875696,2	K562	blood:

Variant related genes	Relation type
PTAR1	TF binding region
ENSG00000107282	Chromatin interaction
ENSG00000100084	Chromatin interaction
ENSG00000198887	Chromatin interaction
ENSG00000143319	Chromatin interaction
ENSG00000242259	Chromatin interaction
ENSG00000143303	Chromatin interaction
ENSG00000261447	Chromatin interaction
ENSG00000185065	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10118222	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10119846	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10217776	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10735560	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10746706	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10746707	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10780585	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10780610	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10867922	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10868056	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11139996	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1330238	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1330240	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1330332	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1411410	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1536992	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1536994	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1547690	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1576482	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1576483	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1980934	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026794	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2150045	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252130	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2274745	0.91[ASN][1000 genomes]
rs2309531	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4535802	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4535803	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7023462	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7037769	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7039383	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7851707	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7867543	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72371800-72375600	Active TSS	Fetal Brain Male	brain
2	chr9:72372200-72375400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:72372400-72375800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr9:72372600-72375600	Active TSS	Fetal Brain Female	brain
5	chr9:72372800-72375600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:72373000-72375200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:72373000-72375400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:72373000-72375400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:72373000-72375600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr9:72373000-72375800	Active TSS	GM12878-XiMat	blood
11	chr9:72373200-72375200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:72373200-72375200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr9:72373200-72375200	Active TSS	HSMM	muscle
14	chr9:72373200-72375200	Active TSS	NHLF	lung
15	chr9:72373200-72375400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:72373200-72375400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:72373200-72375400	Active TSS	Brain Hippocampus Middle	brain
18	chr9:72373200-72375400	Active TSS	HSMMtube	muscle
19	chr9:72373200-72375600	Active TSS	Brain Angular Gyrus	brain
20	chr9:72373200-72375600	Active TSS	Fetal Stomach	stomach
21	chr9:72373200-72375600	Active TSS	Fetal Thymus	thymus
22	chr9:72373200-72375600	Active TSS	Right Ventricle	heart
23	chr9:72373200-72375600	Active TSS	HMEC	breast
24	chr9:72373200-72375600	Active TSS	K562	blood
25	chr9:72373400-72375200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr9:72373400-72375200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:72373400-72375400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr9:72373400-72375400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr9:72373400-72375600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:72373400-72375600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:72373600-72375200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:72373600-72375200	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr9:72373600-72375200	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr9:72373600-72375200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:72373600-72375200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:72373600-72375200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:72373600-72375200	Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr9:72373600-72375200	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr9:72373600-72375200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr9:72373600-72375200	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr9:72373600-72375200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:72373600-72375200	Active TSS	Muscle Satellite Cultured Cells	--
43	chr9:72373600-72375200	Active TSS	Colonic Mucosa	Colon
44	chr9:72373600-72375200	Active TSS	Colon Smooth Muscle	Colon
45	chr9:72373600-72375200	Active TSS	Duodenum Mucosa	Duodenum
46	chr9:72373600-72375200	Active TSS	Pancreas	Pancrea
47	chr9:72373600-72375200	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr9:72373600-72375200	Active TSS	Dnd41	blood
49	chr9:72373600-72375200	Active TSS	Hela-S3	cervix
50	chr9:72373600-72375200	Active TSS	HUVEC	blood vessel

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