Variant report

Variant	rs62392941
Chromosome Location	chr6:29600552-29600553
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	POLR2A	chr6:29599013-29601394	K562	blood:	n/a	n/a
2	POLR2A	chr6:29599751-29601409	PFSK-1	brain:	n/a	n/a
3	YY1	chr6:29600530-29601094	H1-hESC	embryonic stem cell:	n/a	chr6:29600547-29600561
4	POLR2A	chr6:29600518-29601302	HCT-116	colon:	n/a	n/a
5	HMGN3	chr6:29600004-29601481	K562	blood:	n/a	n/a
6	POLR2A	chr6:29600528-29600776	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr6:29600543-29600672	A549	lung:	n/a	n/a
8	ZBTB7A	chr6:29600547-29601309	ECC-1	luminal epithelium:	n/a	chr6:29600581-29600590
9	ZNF263	chr6:29599942-29601366	K562	blood:	n/a	chr6:29600781-29600802
10	ZNF263	chr6:29599102-29601690	HEK293-T-REx	kidney:	n/a	chr6:29600781-29600802
11	TAF1	chr6:29600039-29601736	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr6:29600031-29601407	ProgFib	skin:	n/a	n/a
13	UBTF	chr6:29598709-29601143	K562	blood:	n/a	n/a
14	ZBTB7A	chr6:29600529-29601487	ECC-1	luminal epithelium:	n/a	chr6:29600581-29600590
15	POLR2A	chr6:29600319-29600843	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr6:29599777-29602043	H1-neurons	neurons:	n/a	chr6:29601089-29601102
17	POLR2A	chr6:29598104-29601707	K562	blood:	n/a	n/a
18	POLR2A	chr6:29599663-29601899	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr6:29599885-29601775	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr6:29600010-29601504	HEK293	kidney:	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	JUND	chr6:29600153-29601852	K562	blood:	n/a	n/a
24	E2F6	chr6:29600522-29600688	K562	blood:	n/a	chr6:29600580-29600589
25	POLR2A	chr6:29600349-29600676	A549	lung:	n/a	n/a
26	MAZ	chr6:29600081-29601369	GM12878	blood:	n/a	chr6:29600301-29600311
27	POLR2A	chr6:29599054-29601572	K562	blood:	n/a	n/a
28	POLR2A	chr6:29599853-29601506	PFSK-1	brain:	n/a	n/a
29	UBTF	chr6:29599028-29601472	K562	blood:	n/a	n/a
30	MAZ	chr6:29599759-29601808	IMR90	lung:	n/a	chr6:29600301-29600311 chr6:29601521-29601531
31	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
32	MAZ	chr6:29600065-29601271	Hela-S3	cervix:	n/a	chr6:29600301-29600311
33	SIN3A	chr6:29599830-29601885	H1-hESC	embryonic stem cell:	n/a	chr6:29601213-29601222
34	CCNT2	chr6:29599836-29601284	K562	blood:	n/a	chr6:29600383-29600392 chr6:29601174-29601183 chr6:29600424-29600433 chr6:29600521-29600530 chr6:29600562-29600571
35	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
36	POLR2A	chr6:29599810-29601940	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr6:29600282-29601288	A549	lung:	n/a	n/a
38	POLR2A	chr6:29600544-29601274	HCT-116	colon:	n/a	n/a
39	POLR2A	chr6:29598886-29601567	K562	blood:	n/a	n/a
40	POLR2A	chr6:29600116-29601339	SK-N-SH	brain:	n/a	n/a
41	TBP	chr6:29600192-29601297	K562	blood:	n/a	n/a
42	POLR2A	chr6:29600293-29601468	Raji	blood:	n/a	n/a
43	POLR2A	chr6:29599963-29601343	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr6:29600108-29600594	HUVEC	blood vessel:	n/a	n/a
45	MXI1	chr6:29599718-29601388	IMR90	lung:	n/a	n/a
46	POLR2A	chr6:29600024-29601352	MCF-7	breast:	n/a	n/a
47	POLR2A	chr6:29599004-29601329	K562	blood:	n/a	n/a
48	POLR2A	chr6:29600322-29601230	IMR90	lung:	n/a	n/a
49	MYC	chr6:29600150-29601506	K562	blood:	n/a	chr6:29600301-29600311
50	MAX	chr6:29600075-29600615	MCF-7	breast:	n/a	chr6:29600301-29600311

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
ENSG00000237988	Chromatin interaction
ENSG00000235238	Chromatin interaction
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16895101	0.91[ASN][1000 genomes]
rs2057010	0.96[ASN][1000 genomes]
rs2058325	0.91[ASN][1000 genomes]
rs2058326	0.86[ASN][1000 genomes]
rs28359971	0.88[ASN][1000 genomes]
rs28359972	0.90[ASN][1000 genomes]
rs28749524	0.90[ASN][1000 genomes]
rs29219	0.96[ASN][1000 genomes]
rs29256	0.95[ASN][1000 genomes]
rs29266	0.95[ASN][1000 genomes]
rs3025628	0.96[ASN][1000 genomes]
rs3025642	0.96[ASN][1000 genomes]
rs362515	0.95[ASN][1000 genomes]
rs362517	0.95[ASN][1000 genomes]
rs55701059	0.95[ASN][1000 genomes]
rs55871431	0.95[ASN][1000 genomes]
rs55888673	0.95[ASN][1000 genomes]
rs55971964	0.93[ASN][1000 genomes]
rs56020557	0.91[ASN][1000 genomes]
rs56045105	0.96[ASN][1000 genomes]
rs56106029	0.95[ASN][1000 genomes]
rs56142919	0.96[ASN][1000 genomes]
rs56155438	0.96[ASN][1000 genomes]
rs56393713	0.96[ASN][1000 genomes]
rs62392942	0.93[ASN][1000 genomes]
rs62392943	0.93[ASN][1000 genomes]
rs62406580	0.93[ASN][1000 genomes]
rs62406582	0.95[ASN][1000 genomes]
rs62406583	0.96[ASN][1000 genomes]
rs62406584	0.95[ASN][1000 genomes]
rs72831507	0.95[ASN][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:126 , 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	chr6:29598200-29602000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:29598800-29601600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:29599000-29601800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:29599000-29601800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:29599000-29602400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:29599200-29600600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:29599200-29601400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:29599200-29601800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:29599600-29601200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:29599600-29601600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:29599600-29601600	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr6:29599600-29601600	Active TSS	Aorta	Aorta
14	chr6:29599600-29601800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:29599600-29601800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:29599600-29601800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr6:29599600-29601800	Active TSS	NHLF	lung
18	chr6:29599800-29600600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
19	chr6:29599800-29601200	Active TSS	Brain Anterior Caudate	brain
20	chr6:29599800-29601200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:29599800-29601400	Active TSS	HSMMtube	muscle
22	chr6:29599800-29601800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:29599800-29601800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
24	chr6:29599800-29602600	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr6:29600000-29601000	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
26	chr6:29600000-29601200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:29600000-29601200	Active TSS	Brain Substantia Nigra	brain
28	chr6:29600000-29601200	Weak transcription	Fetal Heart	heart
29	chr6:29600000-29601400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:29600000-29601400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr6:29600000-29601400	Active TSS	Brain Hippocampus Middle	brain
32	chr6:29600000-29601400	Active TSS	Small Intestine	intestine
33	chr6:29600000-29601400	Active TSS	A549	lung
34	chr6:29600000-29601600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:29600000-29601600	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr6:29600000-29601600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:29600000-29601600	Active TSS	Placenta Amnion	Placenta Amnion
38	chr6:29600000-29601600	Active TSS	HSMM	muscle
39	chr6:29600000-29601800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:29600000-29601800	Active TSS	Muscle Satellite Cultured Cells	--
41	chr6:29600000-29601800	Active TSS	Colon Smooth Muscle	Colon
42	chr6:29600000-29601800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr6:29600000-29601800	Active TSS	Fetal Kidney	kidney
44	chr6:29600000-29601800	Active TSS	Rectal Smooth Muscle	rectum
45	chr6:29600000-29601800	Active TSS	NHDF-Ad	bronchial
46	chr6:29600000-29602000	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr6:29600000-29602000	Active TSS	Brain Angular Gyrus	brain
48	chr6:29600000-29602200	Active TSS	Fetal Brain Female	brain
49	chr6:29600200-29600600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr6:29600200-29600600	Bivalent Enhancer	Liver	Liver

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