Variant report

Variant	rs9261280
Chromosome Location	chr6:30034184-30034185
allele	C/T
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	MXI1	chr6:30033682-30035697	IMR90	lung:	n/a	n/a
2	CHD1	chr6:30034180-30035062	GM12878	blood:	n/a	n/a
3	SPI1	chr6:30034170-30035270	GM12878	blood:	n/a	chr6:30034551-30034564 chr6:30034552-30034561 chr6:30034774-30034781 chr6:30035145-30035158
4	REST	chr6:30033943-30035861	H1-neurons	neurons:	n/a	chr6:30034818-30034831
5	POLR2A	chr6:30033888-30035534	HepG2	liver:	n/a	n/a
6	MBD4	chr6:30034055-30035290	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:30034084-30035489	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr6:30033951-30035237	HepG2	liver:	n/a	n/a
9	MAZ	chr6:30034011-30035602	IMR90	lung:	n/a	chr6:30035150-30035160
10	POLR2A	chr6:30034090-30035250	MCF10A-Er-Src	breast:	n/a	n/a
11	HCFC1	chr6:30033948-30035853	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:30033687-30035386	GM12892	blood:	n/a	n/a
13	BCLAF1	chr6:30034109-30035298	GM12878	blood:	n/a	chr6:30034995-30035004
14	POLR2A	chr6:30033681-30035402	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr6:30033996-30035547	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr6:30033747-30035349	GM12892	blood:	n/a	n/a
17	JUN	chr6:30033661-30035734	K562	blood:	n/a	chr6:30035268-30035277 chr6:30035265-30035274
18	POLR2A	chr6:30033875-30035161	K562	blood:	n/a	n/a
19	MTA3	chr6:30034176-30035586	GM12878	blood:	n/a	n/a
20	SPI1	chr6:30034180-30035372	HL-60	blood:	n/a	chr6:30034551-30034564 chr6:30034552-30034561 chr6:30034774-30034781 chr6:30035145-30035158
21	POLR2A	chr6:30034098-30035235	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr6:30033780-30035297	HCT-116	colon:	n/a	n/a
23	POLR2A	chr6:30033932-30035233	GM12878	blood:	n/a	n/a
24	YY1	chr6:30034103-30035267	GM12878	blood:	n/a	chr6:30034408-30034418
25	POLR2A	chr6:30033763-30035352	GM12878	blood:	n/a	n/a
26	MXI1	chr6:30034109-30035434	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:30033738-30035539	K562	blood:	n/a	n/a
28	ELF1	chr6:30034180-30035695	HCT-116	colon:	n/a	chr6:30034979-30034990 chr6:30034979-30034990 chr6:30034994-30035003 chr6:30034551-30034562 chr6:30034981-30034990 chr6:30034993-30035004 chr6:30034980-30034989
29	NFATC1	chr6:30034125-30035223	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:30034172-30035307	GM12892	blood:	n/a	n/a
31	MAX	chr6:30034166-30035565	HepG2	liver:	n/a	chr6:30035150-30035160
32	PML	chr6:30033938-30035309	K562	blood:	n/a	chr6:30034568-30034576
33	POLR2A	chr6:30034150-30035274	Raji	blood:	n/a	n/a
34	POLR2A	chr6:30033685-30035337	PFSK-1	brain:	n/a	n/a
35	IRF1	chr6:30034032-30035218	K562	blood:	n/a	chr6:30034859-30034873 chr6:30034858-30034872 chr6:30034859-30034869 chr6:30034587-30034604 chr6:30034549-30034558
36	MXI1	chr6:30033710-30035798	SK-N-SH	brain:	n/a	n/a
37	MBD4	chr6:30034075-30034863	HepG2	liver:	n/a	n/a
38	NFIC	chr6:30034055-30035708	GM12878	blood:	n/a	n/a
39	PML	chr6:30034067-30035377	GM12878	blood:	n/a	chr6:30034568-30034576
40	ATF2	chr6:30034044-30035216	GM12878	blood:	n/a	n/a
41	EP300	chr6:30034182-30035169	K562	blood:	n/a	chr6:30034548-30034562 chr6:30034860-30034874 chr6:30034996-30035003
42	POLR2A	chr6:30034150-30035497	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr6:30033786-30035526	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr6:30033893-30035254	GM12878	blood:	n/a	n/a
45	YY1	chr6:30034182-30034625	SK-N-SH_RA	brain:	n/a	chr6:30034408-30034418
46	POLR2A	chr6:30034100-30035259	GM12891	blood:	n/a	n/a
47	HDAC2	chr6:30034161-30035251	MCF-7	breast:	n/a	chr6:30034858-30034872
48	ZNF384	chr6:30033984-30034858	GM12878	blood:	n/a	n/a
49	GABPA	chr6:30034108-30035677	MCF-7	breast:	n/a	chr6:30034876-30034885 chr6:30034874-30034885 chr6:30034871-30034885 chr6:30034874-30034888
50	SIN3AK20	chr6:30034123-30035524	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30034178-30034228	H1-hESC	embryonic stem cell:	embryo
2	chr6:30034178-30034228	SK-N-MC	brain:	n/a
3	chr6:30034178-30034228	HUVEC	blood vessel:	n/a
4	chr6:30034178-30034228	IMR90	lung:	fetal
5	chr6:30034178-30034228	AoSMC	blood vessel:	n/a
6	chr6:30034178-30034228	HRCEpiC	kidney:	n/a
7	chr6:30034178-30034228	SKMC	muscle:	n/a
8	chr6:30034178-30034228	SK-N-SH_RA	brain:	n/a
9	chr6:30034178-30034228	AG04449	skin:	fetal
10	chr6:30034178-30034228	HCT-116	colon:	n/a
11	chr6:30034178-30034228	HL-60	blood:	n/a
12	chr6:30034178-30034228	NHDF-neo	bronchial:	n/a
13	chr6:30034178-30034228	AG04450	lung:	fetal
14	chr6:30034178-30034228	HRE	kidney:	n/a
15	chr6:30034178-30034228	BE2_C	brain:	n/a
16	chr6:30034178-30034228	ProgFib	skin:	n/a
17	chr6:30034178-30034228	BJ	skin:	n/a
18	chr6:30034178-30034228	SAEC	small airway:	n/a
19	chr6:30034178-30034228	AG09309	skin:	n/a
20	chr6:30034178-30034228	PrEC	prostate:	n/a
21	chr6:30034178-30034228	MCF-7	breast:	n/a
22	chr6:30034178-30034228	HAEpiC	amniotic membrane:	n/a
23	chr6:30034178-30034228	GM12891	blood:	n/a
24	chr6:30034178-30034228	HCPEpiC	choroid plexus:	n/a
25	chr6:30034178-30034228	Jurkat	blood:	n/a
26	chr6:30034178-30034228	A549	lung:	n/a
27	chr6:30034178-30034228	MCF10A-Er-Src	breast:	n/a
28	chr6:30034178-30034228	GM12878	blood:	n/a
29	chr6:30034178-30034228	NHBE	bronchial:	n/a
30	chr6:30034178-30034228	HCM	heart:	n/a
31	chr6:30034178-30034228	ECC-1	luminal epithelium:	n/a
32	chr6:30034178-30034228	U87	brain:	n/a
33	chr6:30034178-30034228	T-47D	breast:	n/a
34	chr6:30034178-30034228	HepG2	liver:	n/a
35	chr6:30034178-30034228	NH-A	brain:	n/a
36	chr6:30034178-30034228	GM19239	blood:	n/a
37	chr6:30034178-30034228	Caco-2	colon:	n/a
38	chr6:30034178-30034228	HEK293	kidney:	embryo
39	chr6:30034178-30034228	GM12892	blood:	n/a
40	chr6:30034178-30034228	Hepatocyte	liver:	n/a
41	chr6:30034178-30034228	LNCaP	prostate:	n/a
42	chr6:30034178-30034228	HRPEpiC	eye:	n/a
43	chr6:30034178-30034228	RPTEC	kidney:	n/a
44	chr6:30034178-30034228	NT2-D1	testis:	n/a
45	chr6:30034178-30034228	GM06990	blood:	n/a
46	chr6:30034178-30034228	HNPCEpiC	eye:	n/a
47	chr6:30034178-30034228	AG09319	gingival:	n/a
48	chr6:30034178-30034228	HCF	heart:	n/a
49	chr6:30034178-30034228	HPAEpiC	pulmonary alveolar:	n/a
50	chr6:30034178-30034228	HIPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30033185..30035212-chr6:30180473..30182741,2	MCF-7	breast:
2	chr6:30032984..30034592-chr6:30523078..30524933,2	K562	blood:
3	chr6:30033618..30036318-chr6:30097659..30102068,3	MCF-7	breast:

Variant related genes	Relation type
PPP1R11	TF binding region
ZNRD1-AS1	TF binding region
ZNRD1-AS1	CpG island
PPP1R11	CpG island
ENSG00000234127	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000252228	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12210298	1.00[ASN][1000 genomes]
rs28400886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260673	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9260679	0.97[EUR][1000 genomes]
rs9260705	0.97[EUR][1000 genomes]
rs9260770	0.97[EUR][1000 genomes]
rs9260802	1.00[EUR][1000 genomes]
rs9260811	1.00[EUR][1000 genomes]
rs9260888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260924	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261267	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30030000-30034200	Weak transcription	Left Ventricle	heart
2	chr6:30030000-30034200	Weak transcription	Ovary	ovary
3	chr6:30030200-30034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:30030200-30034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:30030200-30034200	Weak transcription	Lung	lung
6	chr6:30030200-30034400	Weak transcription	Spleen	Spleen
7	chr6:30030800-30034400	Weak transcription	Gastric	stomach
8	chr6:30033600-30034200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:30033600-30034200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr6:30033600-30034200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:30033600-30034200	Enhancers	Brain Substantia Nigra	brain
12	chr6:30033600-30034200	Flanking Active TSS	Fetal Brain Female	brain
13	chr6:30033600-30034200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr6:30033600-30034200	Flanking Active TSS	GM12878-XiMat	blood
15	chr6:30033600-30034400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:30033600-30034400	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr6:30033600-30034400	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr6:30033600-30034400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr6:30033600-30034400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr6:30033600-30034400	Flanking Active TSS	Dnd41	blood
21	chr6:30033600-30034600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr6:30033600-30034600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr6:30033600-30034600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:30033600-30034600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:30033600-30035800	Active TSS	A549	lung
26	chr6:30033800-30034200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:30033800-30034200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:30033800-30034200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr6:30033800-30034200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:30033800-30034200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:30033800-30034200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr6:30033800-30034200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:30033800-30034200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr6:30033800-30034200	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr6:30033800-30034200	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr6:30033800-30034200	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr6:30033800-30034200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr6:30033800-30034200	Flanking Active TSS	Fetal Brain Male	brain
39	chr6:30033800-30034200	Flanking Active TSS	Fetal Kidney	kidney
40	chr6:30033800-30034200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr6:30033800-30034200	Enhancers	Placenta	Placenta
42	chr6:30033800-30034200	Flanking Active TSS	Psoas Muscle	Psoas
43	chr6:30033800-30034200	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr6:30033800-30034200	Flanking Active TSS	HepG2	liver
45	chr6:30033800-30034200	Flanking Active TSS	HSMMtube	muscle
46	chr6:30033800-30034200	Flanking Active TSS	K562	blood
47	chr6:30033800-30034200	Flanking Active TSS	NHDF-Ad	bronchial
48	chr6:30033800-30034400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:30033800-30034400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr6:30033800-30034400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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