Variant report

Variant	rs6729945
Chromosome Location	chr2:172864695-172864696
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	CTCF	chr2:172864580-172864730	HepG2	liver:	n/a	n/a
2	TBL1XR1	chr2:172864543-172865358	GM12878	blood:	n/a	n/a
3	REST	chr2:172864546-172865635	HL-60	blood:	n/a	chr2:172865495-172865509 chr2:172865489-172865509
4	TCF12	chr2:172864671-172865047	GM12878	blood:	n/a	n/a
5	SIX5	chr2:172864512-172865440	A549	lung:	n/a	n/a
6	POLR2A	chr2:172864398-172865312	PANC-1	pancreas:	n/a	n/a
7	REST	chr2:172864668-172865080	SK-N-SH	brain:	n/a	n/a
8	PML	chr2:172864340-172865439	K562	blood:	n/a	n/a
9	TAF1	chr2:172864462-172865149	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:172864476-172865378	HepG2	liver:	n/a	n/a
11	RAD21	chr2:172864481-172865242	IMR90	lung:	n/a	chr2:172864823-172864836
12	NFIC	chr2:172864386-172865466	HepG2	liver:	n/a	n/a
13	MAX	chr2:172864353-172865534	HCT-116	colon:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
14	NRF1	chr2:172864670-172865052	HepG2	liver:	n/a	chr2:172864828-172864837 chr2:172864755-172864766
15	NFIC	chr2:172864576-172865514	HepG2	liver:	n/a	n/a
16	MAX	chr2:172864520-172865468	A549	lung:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
17	CTCF	chr2:172864580-172864730	GM12871	blood:	n/a	n/a
18	RAD21	chr2:172864490-172865230	SK-N-SH_RA	brain:	n/a	chr2:172864823-172864836
19	POLR2A	chr2:172864534-172865136	A549	lung:	n/a	n/a
20	SIX5	chr2:172864689-172865173	A549	lung:	n/a	n/a
21	RCOR1	chr2:172864610-172865221	GM12878	blood:	n/a	n/a
22	BCL3	chr2:172864390-172865401	A549	lung:	n/a	n/a
23	POLR2A	chr2:172864487-172865324	ProgFib	skin:	n/a	n/a
24	TEAD4	chr2:172864622-172865306	K562	blood:	n/a	n/a
25	POLR2A	chr2:172864511-172865205	HepG2	liver:	n/a	n/a
26	YY1	chr2:172864609-172865454	A549	lung:	n/a	chr2:172864825-172864839 chr2:172864866-172864886 chr2:172864828-172864842
27	POLR2A	chr2:172864476-172865170	HCT-116	colon:	n/a	n/a
28	NRF1	chr2:172864319-172865228	SK-N-SH	brain:	n/a	chr2:172864828-172864837 chr2:172864755-172864766
29	YY1	chr2:172864422-172865261	K562	blood:	n/a	chr2:172864825-172864839 chr2:172864866-172864886 chr2:172864828-172864842
30	HEY1	chr2:172864543-172865613	HepG2	liver:	n/a	n/a
31	USF1	chr2:172864428-172865303	SK-N-SH	brain:	n/a	chr2:172864856-172864867 chr2:172864823-172864839
32	RAD21	chr2:172864503-172865350	A549	lung:	n/a	chr2:172864823-172864836
33	TBL1XR1	chr2:172864349-172865814	K562	blood:	n/a	n/a
34	MYC	chr2:172864538-172865500	Hela-S3	cervix:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
35	HCFC1	chr2:172864424-172865446	Hela-S3	cervix:	n/a	n/a
36	YY1	chr2:172864552-172865356	K562	blood:	n/a	chr2:172864825-172864839 chr2:172864866-172864886 chr2:172864828-172864842
37	TEAD4	chr2:172864644-172865150	H1-hESC	embryonic stem cell:	n/a	n/a
38	MYC	chr2:172864610-172865310	MCF-7	breast:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
39	HEY1	chr2:172864425-172865301	K562	blood:	n/a	n/a
40	CTCF	chr2:172864640-172864721	MCF-7	breast:	n/a	n/a
41	POLR2A	chr2:172864429-172865408	K562	blood:	n/a	n/a
42	POLR2A	chr2:172864557-172865131	SK-N-SH	brain:	n/a	n/a
43	CTCF	chr2:172864600-172864750	GM12871	blood:	n/a	n/a
44	ELF1	chr2:172864589-172865039	K562	blood:	n/a	n/a
45	TAF1	chr2:172864427-172865370	ECC-1	luminal epithelium:	n/a	n/a
46	CTCF	chr2:172864580-172864730	NHEK	skin:	n/a	n/a
47	CTCF	chr2:172864560-172864710	AoAF	blood vessel:	n/a	n/a
48	MYC	chr2:172864639-172865486	K562	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
49	ZNF143	chr2:172864626-172865039	GM12878	blood:	n/a	n/a
50	TAF1	chr2:172864509-172865303	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:172863381..172865132-chr2:172924958..172927915,2	MCF-7	breast:
2	chr2:172863226..172865802-chr2:172966081..172969208,5	MCF-7	breast:
3	chr2:172860607..172867322-chr2:172946572..172954768,24	MCF-7	breast:
4	chr2:172863189..172867097-chr2:172945137..172953576,15	K562	blood:
5	chr2:172777448..172780536-chr2:172864307..172867165,5	K562	blood:
6	chr2:172777448..172780686-chr2:172863264..172866650,5	K562	blood:
7	chr2:172859788..172868192-chr2:172944876..172951443,18	MCF-7	breast:
8	chr2:172861569..172867068-chr2:172965912..172971063,13	K562	blood:
9	chr2:172863189..172870519-chr2:172946500..172952655,22	K562	blood:
10	chr2:172377500..172380432-chr2:172864656..172866178,2	K562	blood:
11	chr2:172749212..172752099-chr2:172863500..172865923,3	MCF-7	breast:
12	chr11:65265208..65268065-chr2:172864519..172866349,2	MCF-7	breast:
13	chr2:172862808..172868920-chr2:172961807..172971063,13	K562	blood:

Variant related genes	Relation type
METAP1D	TF binding region
ENSG00000128708	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000236651	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000071967	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000270117	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11676438	0.82[AMR][1000 genomes]
rs55653103	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62182436	0.83[AMR][1000 genomes]
rs62183769	0.85[AMR][1000 genomes]
rs62183770	0.85[AMR][1000 genomes]
rs62183782	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62183783	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183784	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183785	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183800	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183801	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6718013	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6730085	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6733794	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6737308	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6746701	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557612	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7584187	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7598246	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6729945	AC068039.4	cis	Muscle Skeletal	GTEx
rs6729945	AC068039.4	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172863600-172865600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:172863800-172865400	Active TSS	Brain Anterior Caudate	brain
3	chr2:172864000-172865200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr2:172864000-172865400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:172864000-172865600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr2:172864000-172865600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:172864000-172865800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:172864000-172865800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr2:172864000-172865800	Active TSS	A549	lung
10	chr2:172864200-172864800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr2:172864200-172864800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:172864200-172865200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:172864200-172865200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:172864200-172865200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:172864200-172865200	Active TSS	Colonic Mucosa	Colon
16	chr2:172864200-172865200	Active TSS	NH-A	brain
17	chr2:172864200-172865400	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr2:172864200-172865400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:172864200-172865400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr2:172864200-172865400	Active TSS	Fetal Brain Male	brain
21	chr2:172864200-172865400	Active TSS	Stomach Smooth Muscle	stomach
22	chr2:172864200-172865600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:172864200-172865600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:172864200-172865600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:172864200-172865600	Active TSS	Fetal Brain Female	brain
26	chr2:172864200-172865600	Active TSS	Fetal Muscle Trunk	muscle
27	chr2:172864200-172865600	Active TSS	Ovary	ovary
28	chr2:172864200-172865600	Active TSS	Psoas Muscle	Psoas
29	chr2:172864200-172865600	Active TSS	Right Atrium	heart
30	chr2:172864200-172865600	Active TSS	HSMMtube	muscle
31	chr2:172864200-172865600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr2:172864200-172866000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:172864400-172865000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:172864400-172865000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:172864400-172865000	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr2:172864400-172865000	Active TSS	HepG2	liver
37	chr2:172864400-172865200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr2:172864400-172865200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:172864400-172865200	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:172864400-172865200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:172864400-172865200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr2:172864400-172865200	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr2:172864400-172865200	Active TSS	Brain Substantia Nigra	brain
44	chr2:172864400-172865200	Active TSS	Fetal Intestine Small	intestine
45	chr2:172864400-172865200	Active TSS	Fetal Muscle Leg	muscle
46	chr2:172864400-172865200	Active TSS	Placenta	Placenta
47	chr2:172864400-172865200	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr2:172864400-172865200	Active TSS	Rectal Smooth Muscle	rectum
49	chr2:172864400-172865200	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr2:172864400-172865200	Active TSS	Hela-S3	cervix

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