Variant report

Variant	rs56034620
Chromosome Location	chr6:29600124-29600125
allele	A/G/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	POLR2A	chr6:29599013-29601394	K562	blood:	n/a	n/a
2	POLR2A	chr6:29599751-29601409	PFSK-1	brain:	n/a	n/a
3	HMGN3	chr6:29600004-29601481	K562	blood:	n/a	n/a
4	EGR1	chr6:29599933-29600506	HCT-116	colon:	n/a	chr6:29600304-29600313 chr6:29600297-29600319 chr6:29600302-29600316 chr6:29600300-29600310 chr6:29600301-29600314 chr6:29600295-29600308 chr6:29600301-29600314 chr6:29600300-29600315 chr6:29600424-29600434 chr6:29600301-29600315 chr6:29600304-29600314 chr6:29600301-29600314 chr6:29600302-29600313 chr6:29600301-29600314
5	ZNF263	chr6:29599942-29601366	K562	blood:	n/a	chr6:29600781-29600802
6	IRF1	chr6:29599864-29600485	K562	blood:	n/a	chr6:29600299-29600313 chr6:29600031-29600040 chr6:29600305-29600319
7	ZNF263	chr6:29599102-29601690	HEK293-T-REx	kidney:	n/a	chr6:29600781-29600802
8	TAF1	chr6:29600039-29601736	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr6:29600031-29601407	ProgFib	skin:	n/a	n/a
10	UBTF	chr6:29598709-29601143	K562	blood:	n/a	n/a
11	POLR2A	chr6:29600031-29600526	K562	blood:	n/a	n/a
12	REST	chr6:29599777-29602043	H1-neurons	neurons:	n/a	chr6:29601089-29601102
13	POLR2A	chr6:29598104-29601707	K562	blood:	n/a	n/a
14	E2F6	chr6:29600074-29600393	K562	blood:	n/a	chr6:29600201-29600210 chr6:29600197-29600206 chr6:29600300-29600309
15	POLR2A	chr6:29599663-29601899	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr6:29599885-29601775	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr6:29600010-29601504	HEK293	kidney:	n/a	n/a
18	MAX	chr6:29599937-29600480	K562	blood:	n/a	chr6:29600301-29600311
19	SIN3AK20	chr6:29599759-29600331	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:29600054-29600310	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr6:29599784-29601365	K562	blood:	n/a	n/a
22	MAZ	chr6:29598835-29601887	K562	blood:	n/a	chr6:29600301-29600311 chr6:29601521-29601531
23	MAZ	chr6:29600081-29601369	GM12878	blood:	n/a	chr6:29600301-29600311
24	POLR2A	chr6:29600094-29600520	K562	blood:	n/a	n/a
25	POLR2A	chr6:29599054-29601572	K562	blood:	n/a	n/a
26	SPI1	chr6:29599924-29600140	K562	blood:	n/a	chr6:29600025-29600038
27	POLR2A	chr6:29599853-29601506	PFSK-1	brain:	n/a	n/a
28	UBTF	chr6:29599028-29601472	K562	blood:	n/a	n/a
29	MYC	chr6:29600074-29600223	MCF10A-Er-Src	breast:	n/a	n/a
30	EGR1	chr6:29600066-29600541	MCF-7	breast:	n/a	chr6:29600304-29600313 chr6:29600297-29600319 chr6:29600302-29600316 chr6:29600300-29600310 chr6:29600301-29600314 chr6:29600295-29600308 chr6:29600301-29600314 chr6:29600300-29600315 chr6:29600424-29600434 chr6:29600301-29600315 chr6:29600304-29600314 chr6:29600301-29600314 chr6:29600302-29600313 chr6:29600301-29600314
31	MAZ	chr6:29599759-29601808	IMR90	lung:	n/a	chr6:29600301-29600311 chr6:29601521-29601531
32	EGR1	chr6:29599993-29600592	K562	blood:	n/a	chr6:29600304-29600313 chr6:29600297-29600319 chr6:29600302-29600316 chr6:29600300-29600310 chr6:29600301-29600314 chr6:29600295-29600308 chr6:29600301-29600314 chr6:29600300-29600315 chr6:29600424-29600434 chr6:29600301-29600315 chr6:29600304-29600314 chr6:29600301-29600314 chr6:29600302-29600313 chr6:29600301-29600314 chr6:29600548-29600558 chr6:29600563-29600576
33	MAZ	chr6:29600065-29601271	Hela-S3	cervix:	n/a	chr6:29600301-29600311
34	SIN3A	chr6:29599830-29601885	H1-hESC	embryonic stem cell:	n/a	chr6:29601213-29601222
35	CCNT2	chr6:29599836-29601284	K562	blood:	n/a	chr6:29600383-29600392 chr6:29601174-29601183 chr6:29600424-29600433 chr6:29600521-29600530 chr6:29600562-29600571
36	POLR2A	chr6:29600112-29600520	U87	brain:	n/a	n/a
37	EGR1	chr6:29599962-29600581	HCT-116	colon:	n/a	chr6:29600304-29600313 chr6:29600297-29600319 chr6:29600302-29600316 chr6:29600300-29600310 chr6:29600301-29600314 chr6:29600295-29600308 chr6:29600301-29600314 chr6:29600300-29600315 chr6:29600424-29600434 chr6:29600301-29600315 chr6:29600304-29600314 chr6:29600301-29600314 chr6:29600302-29600313 chr6:29600301-29600314 chr6:29600548-29600558 chr6:29600563-29600576
38	POLR2A	chr6:29599810-29601940	H1-neurons	neurons:	n/a	n/a
39	RCOR1	chr6:29599870-29600443	K562	blood:	n/a	n/a
40	POLR2A	chr6:29598886-29601567	K562	blood:	n/a	n/a
41	POLR2A	chr6:29600116-29601339	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr6:29599963-29601343	HUVEC	blood vessel:	n/a	n/a
43	HCFC1	chr6:29600049-29600394	K562	blood:	n/a	n/a
44	POLR2A	chr6:29600108-29600594	HUVEC	blood vessel:	n/a	n/a
45	EGR1	chr6:29600095-29600519	K562	blood:	n/a	chr6:29600304-29600313 chr6:29600297-29600319 chr6:29600302-29600316 chr6:29600300-29600310 chr6:29600301-29600314 chr6:29600295-29600308 chr6:29600301-29600314 chr6:29600300-29600315 chr6:29600424-29600434 chr6:29600301-29600315 chr6:29600304-29600314 chr6:29600301-29600314 chr6:29600302-29600313 chr6:29600301-29600314
46	MXI1	chr6:29599718-29601388	IMR90	lung:	n/a	n/a
47	POLR2A	chr6:29600024-29601352	MCF-7	breast:	n/a	n/a
48	POLR2A	chr6:29599004-29601329	K562	blood:	n/a	n/a
49	ZBTB7A	chr6:29599946-29600390	ECC-1	luminal epithelium:	n/a	n/a
50	EGR1	chr6:29600081-29600512	ECC-1	luminal epithelium:	n/a	chr6:29600304-29600313 chr6:29600297-29600319 chr6:29600302-29600316 chr6:29600300-29600310 chr6:29600301-29600314 chr6:29600295-29600308 chr6:29600301-29600314 chr6:29600300-29600315 chr6:29600424-29600434 chr6:29600301-29600315 chr6:29600304-29600314 chr6:29600301-29600314 chr6:29600302-29600313 chr6:29600301-29600314

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29600114-29600164	ProgFib	skin:	n/a
2	chr6:29600108-29600158	ECC-1	luminal epithelium:	n/a
3	chr6:29600114-29600164	PANC-1	pancreas:	n/a
4	chr6:29600103-29600153	BE2_C	brain:	n/a
5	chr6:29600112-29600162	AG09319	gingival:	n/a
6	chr6:29600108-29600158	Hepatocyte	liver:	n/a
7	chr6:29600114-29600164	A549	lung:	n/a
8	chr6:29600112-29600162	MCF-7	breast:	n/a
9	chr6:29600103-29600153	ProgFib	skin:	n/a
10	chr6:29600103-29600153	NT2-D1	testis:	n/a
11	chr6:29600114-29600164	HRPEpiC	eye:	n/a
12	chr6:29600103-29600153	LNCaP	prostate:	n/a
13	chr6:29600108-29600158	HPAEpiC	pulmonary alveolar:	n/a
14	chr6:29600112-29600162	SKMC	muscle:	n/a
15	chr6:29600108-29600158	HAEpiC	amniotic membrane:	n/a
16	chr6:29600114-29600164	IMR90	lung:	fetal
17	chr6:29600108-29600158	AG04450	lung:	fetal
18	chr6:29600112-29600162	ovcar-3	ovarian:	n/a
19	chr6:29600108-29600158	HRPEpiC	eye:	n/a
20	chr6:29600108-29600158	NHDF-neo	bronchial:	n/a
21	chr6:29600103-29600153	Caco-2	colon:	n/a
22	chr6:29600112-29600162	A549	lung:	n/a
23	chr6:29600103-29600153	MCF10A-Er-Src	breast:	n/a
24	chr6:29600114-29600164	RPTEC	kidney:	n/a
25	chr6:29600112-29600162	HepG2	liver:	n/a
26	chr6:29600103-29600153	K562	blood:	n/a
27	chr6:29600114-29600164	SK-N-MC	brain:	n/a
28	chr6:29600103-29600153	AG04450	lung:	fetal
29	chr6:29600108-29600158	U87	brain:	n/a
30	chr6:29600114-29600164	GM12878	blood:	n/a
31	chr6:29600108-29600158	HEEpiC	esophagus:	n/a
32	chr6:29600112-29600162	ECC-1	luminal epithelium:	n/a
33	chr6:29600112-29600162	GM06990	blood:	n/a
34	chr6:29600108-29600158	MCF-7	breast:	n/a
35	chr6:29600112-29600162	HEEpiC	esophagus:	n/a
36	chr6:29600103-29600153	AoSMC	blood vessel:	n/a
37	chr6:29600108-29600158	GM06990	blood:	n/a
38	chr6:29600114-29600164	HPAEpiC	pulmonary alveolar:	n/a
39	chr6:29600112-29600162	HIPEpiC	eye:	n/a
40	chr6:29600103-29600153	T-47D	breast:	n/a
41	chr6:29600108-29600158	IMR90	lung:	fetal
42	chr6:29600108-29600158	HepG2	liver:	n/a
43	chr6:29600112-29600162	NHDF-neo	bronchial:	n/a
44	chr6:29600112-29600162	Hepatocyte	liver:	n/a
45	chr6:29600114-29600164	T-47D	breast:	n/a
46	chr6:29600114-29600164	NB4	blood:	n/a
47	chr6:29600112-29600162	HL-60	blood:	n/a
48	chr6:29600108-29600158	HCT-116	colon:	n/a
49	chr6:29600114-29600164	HNPCEpiC	eye:	n/a
50	chr6:29600103-29600153	NH-A	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:29599687..29601377-chr6:29602858..29604767,2	K562	blood:
2	chr6:29520442..29521980-chr6:29599358..29601313,2	MCF-7	breast:
3	chr6:29589009..29590540-chr6:29598383..29601313,2	MCF-7	breast:
4	chr6:29598892..29601377-chr6:29602879..29604767,2	K562	blood:

Variant related genes	Relation type
GABBR1	TF binding region
GABBR1	CpG island
ENSG00000237988	Chromatin interaction
ENSG00000204681	Chromatin interaction
ENSG00000235238	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11968109	1.00[EUR][1000 genomes]
rs16894941	1.00[EUR][1000 genomes]
rs56062033	1.00[EUR][1000 genomes]
rs60225580	1.00[EUR][1000 genomes]
rs61730326	1.00[EUR][1000 genomes]
rs61730328	1.00[EUR][1000 genomes]
rs61730332	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 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	chr6:29597600-29602200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:29598200-29600200	Flanking Active TSS	HMEC	breast
3	chr6:29598200-29602000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:29598400-29600200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr6:29598800-29600200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:29598800-29600200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
7	chr6:29598800-29601600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:29599000-29600200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:29599000-29600200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:29599000-29600200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:29599000-29600200	Flanking Active TSS	HUVEC	blood vessel
12	chr6:29599000-29600200	Flanking Active TSS	K562	blood
13	chr6:29599000-29600400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:29599000-29601800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:29599000-29601800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:29599000-29602400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr6:29599200-29600200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:29599200-29600200	Flanking Active TSS	NH-A	brain
19	chr6:29599200-29600600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:29599200-29601400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:29599200-29601800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr6:29599400-29600200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:29599400-29600200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr6:29599400-29600200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:29599400-29600200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:29599400-29600200	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr6:29599400-29600400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr6:29599600-29600200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
29	chr6:29599600-29600200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr6:29599600-29600200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr6:29599600-29600200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr6:29599600-29600200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:29599600-29600200	Flanking Active TSS	Fetal Brain Male	brain
34	chr6:29599600-29600200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
35	chr6:29599600-29600200	Flanking Active TSS	NHEK	skin
36	chr6:29599600-29600400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
37	chr6:29599600-29600400	Flanking Active TSS	Osteobl	bone
38	chr6:29599600-29601200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:29599600-29601600	Active TSS	H1 Cell Line	embryonic stem cell
40	chr6:29599600-29601600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr6:29599600-29601600	Active TSS	Aorta	Aorta
42	chr6:29599600-29601800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:29599600-29601800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:29599600-29601800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr6:29599600-29601800	Active TSS	NHLF	lung
46	chr6:29599800-29600200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:29599800-29600200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:29599800-29600200	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr6:29599800-29600200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
50	chr6:29599800-29600200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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