Variant report

Variant	rs10761372
Chromosome Location	chr9:97807085-97807086
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	MAX	chr9:97806601-97808755	A549	lung:	n/a	n/a
2	EP300	chr9:97806767-97808285	A549	lung:	n/a	n/a
3	SP1	chr9:97806901-97807778	A549	lung:	n/a	n/a
4	FOSL2	chr9:97806948-97807860	A549	lung:	n/a	n/a
5	POLR2A	chr9:97806952-97807769	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr9:97806933-97807902	A549	lung:	n/a	n/a
7	JUND	chr9:97806830-97807858	A549	lung:	n/a	n/a
8	TCF12	chr9:97806979-97807581	A549	lung:	n/a	n/a
9	JUND	chr9:97807037-97807741	A549	lung:	n/a	n/a
10	RAD21	chr9:97806977-97807742	H1-hESC	embryonic stem cell:	n/a	chr9:97807067-97807076 chr9:97807524-97807538 chr9:97807599-97807613 chr9:97807635-97807648
11	TCF12	chr9:97806630-97809069	A549	lung:	n/a	chr9:97807931-97807941 chr9:97807799-97807806 chr9:97807952-97807959 chr9:97806906-97806914
12	NR3C1	chr9:97807083-97807775	A549	lung:	n/a	n/a
13	ATF3	chr9:97806811-97808484	A549	lung:	n/a	n/a
14	BCL3	chr9:97805869-97809192	A549	lung:	n/a	chr9:97807640-97807649
15	POLR2A	chr9:97806754-97807970	A549	lung:	n/a	n/a
16	POLR2A	chr9:97806684-97807769	HepG2	liver:	n/a	n/a
17	REST	chr9:97807012-97807936	A549	lung:	n/a	chr9:97807375-97807382 chr9:97807547-97807560
18	POLR2A	chr9:97806967-97807252	ProgFib	skin:	n/a	n/a
19	POLR2A	chr9:97806627-97808676	A549	lung:	n/a	n/a
20	YY1	chr9:97806982-97807295	A549	lung:	n/a	n/a
21	FOXA2	chr9:97806965-97807910	A549	lung:	n/a	n/a
22	CEBPB	chr9:97807023-97807509	A549	lung:	n/a	chr9:97807199-97807216
23	MAX	chr9:97806741-97807803	A549	lung:	n/a	n/a
24	POLR2A	chr9:97806868-97807135	A549	lung:	n/a	n/a
25	CTCF	chr9:97806804-97809298	A549	lung:	n/a	chr9:97808280-97808298 chr9:97807606-97807619 chr9:97807066-97807075 chr9:97807801-97807814 chr9:97807525-97807538
26	RAD21	chr9:97807036-97807790	A549	lung:	n/a	chr9:97807779-97807788 chr9:97807067-97807076 chr9:97807524-97807538 chr9:97807599-97807613 chr9:97807635-97807648
27	CEBPB	chr9:97807030-97807646	A549	lung:	n/a	chr9:97807199-97807216
28	BCL3	chr9:97806825-97808589	A549	lung:	n/a	chr9:97807640-97807649
29	CEBPB	chr9:97806948-97807706	A549	lung:	n/a	chr9:97807199-97807216
30	POLR2A	chr9:97807002-97807563	Hela-S3	cervix:	n/a	n/a
31	NR3C1	chr9:97806950-97807618	A549	lung:	n/a	n/a
32	POLR2A	chr9:97806834-97807872	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr9:97806753-97807120	MCF-7	breast:	n/a	n/a
34	GATA3	chr9:97806950-97808848	A549	lung:	n/a	chr9:97808744-97808760 chr9:97807485-97807495 chr9:97808749-97808756 chr9:97808749-97808756 chr9:97808749-97808756 chr9:97808471-97808481 chr9:97808470-97808482 chr9:97808742-97808763
35	FOXA2	chr9:97806882-97807363	A549	lung:	n/a	n/a
36	POLR2A	chr9:97806891-97807991	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97805704..97807873-chr9:97845688..97847934,2	MCF-7	breast:
2	chr9:97805422..97807754-chr9:97822770..97825763,2	MCF-7	breast:
3	chr9:97803206..97809214-chr9:97809347..97813672,8	MCF-7	breast:
4	chr9:97763979..97769403-chr9:97805439..97812937,10	MCF-7	breast:
5	chr9:97802158..97803981-chr9:97806425..97808316,2	K562	blood:
6	chr9:97805980..97807545-chr9:97820488..97822005,2	MCF-7	breast:
7	chr9:97804181..97807973-chr9:97809683..97813710,4	K562	blood:
8	chr9:97806251..97809142-chr9:97810861..97813740,3	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000207864	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000207563	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1004373	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10117370	0.80[ASN][1000 genomes]
rs10119512	0.80[ASN][1000 genomes]
rs1020963	0.95[ASN][1000 genomes]
rs10761368	0.95[ASN][1000 genomes]
rs10993464	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1113102	0.81[ASN][1000 genomes]
rs1412488	0.95[ASN][1000 genomes]
rs1564234	0.81[ASN][1000 genomes]
rs3802454	0.81[ASN][1000 genomes]
rs4743979	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4743980	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4743981	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4743982	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4743984	0.80[ASN][1000 genomes]
rs4744422	0.90[ASN][1000 genomes]
rs4744426	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4744430	0.80[ASN][1000 genomes]
rs4744431	0.98[ASN][1000 genomes]
rs6479588	0.90[ASN][1000 genomes]
rs6479591	0.84[AFR][1000 genomes]
rs6479592	0.84[AFR][1000 genomes]
rs7048786	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7048941	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7854831	0.82[AFR][1000 genomes]
rs7857679	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7862156	0.80[ASN][1000 genomes]
rs7863291	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7871218	0.80[ASN][1000 genomes]
rs7873479	0.91[ASN][1000 genomes]
rs7873567	0.96[AFR][1000 genomes];1.00[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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
3	chr9:97795000-97810400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:97795600-97808600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:97797000-97807800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:97798200-97808600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:97799400-97807600	Weak transcription	Thymus	Thymus
8	chr9:97799400-97810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:97800000-97808600	Genic enhancers	Liver	Liver
10	chr9:97801600-97810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:97802200-97807600	Strong transcription	HSMM	muscle
12	chr9:97802400-97807200	Strong transcription	HSMMtube	muscle
13	chr9:97803000-97810800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:97803400-97807600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:97804000-97807200	Enhancers	Pancreas	Pancrea
16	chr9:97804000-97808800	Weak transcription	Fetal Kidney	kidney
17	chr9:97804000-97810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:97804200-97807800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:97804400-97810400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:97804400-97810800	Weak transcription	K562	blood
21	chr9:97804600-97807200	Genic enhancers	HepG2	liver
22	chr9:97804800-97808200	Strong transcription	NH-A	brain
23	chr9:97804800-97808200	Strong transcription	NHLF	lung
24	chr9:97805000-97810000	Weak transcription	Brain Anterior Caudate	brain
25	chr9:97805200-97807200	Strong transcription	Hela-S3	cervix
26	chr9:97805200-97808400	Genic enhancers	Fetal Intestine Small	intestine
27	chr9:97805200-97810400	Weak transcription	Brain Angular Gyrus	brain
28	chr9:97805400-97807200	Weak transcription	Aorta	Aorta
29	chr9:97805400-97810600	Weak transcription	Small Intestine	intestine
30	chr9:97805600-97810800	Weak transcription	GM12878-XiMat	blood
31	chr9:97806000-97807400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:97806000-97807400	Genic enhancers	Brain Substantia Nigra	brain
33	chr9:97806000-97807400	Genic enhancers	Fetal Lung	lung
34	chr9:97806000-97807600	Genic enhancers	Brain Hippocampus Middle	brain
35	chr9:97806000-97807600	Genic enhancers	Lung	lung
36	chr9:97806000-97807800	Strong transcription	Adipose Nuclei	Adipose
37	chr9:97806000-97808000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:97806000-97808000	Enhancers	Right Atrium	heart
39	chr9:97806000-97808200	Genic enhancers	Fetal Stomach	stomach
40	chr9:97806000-97808400	Genic enhancers	Fetal Intestine Large	intestine
41	chr9:97806200-97807200	Genic enhancers	Brain Cingulate Gyrus	brain
42	chr9:97806200-97807200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr9:97806200-97807400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
44	chr9:97806200-97807600	Genic enhancers	Ovary	ovary
45	chr9:97806200-97807600	Strong transcription	NHDF-Ad	bronchial
46	chr9:97806200-97807800	Genic enhancers	Placenta	Placenta
47	chr9:97806200-97808000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr9:97806200-97808000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
49	chr9:97806200-97808000	Genic enhancers	Osteobl	bone
50	chr9:97806200-97808200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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