Variant report

Variant	rs7549723
Chromosome Location	chr1:150541812-150541813
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr1:150541539-150541904	K562	blood:	n/a	n/a
2	POLR2A	chr1:150538973-150541826	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:150538698-150546656	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:150540015-150541903	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
6	POLR2A	chr1:150538866-150546573	U87	brain:	n/a	n/a
7	POLR2A	chr1:150539774-150546448	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:150540237-150541916	MCF-7	breast:	n/a	n/a
9	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
11	STAT3	chr1:150541722-150541910	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr1:150540216-150546538	U87	brain:	n/a	n/a
13	POLR2A	chr1:150538654-150552953	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:150539727-150546572	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:150538736-150552926	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:150538866-150553173	U87	brain:	n/a	n/a
18	POLR2A	chr1:150540609-150543144	K562	blood:	n/a	n/a
19	POLR2A	chr1:150538945-150546560	HUVEC	blood vessel:	n/a	n/a
20	FOS	chr1:150541703-150543064	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:150541776-150541885	A549	lung:	n/a	n/a
22	POLR2A	chr1:150538877-150553278	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:150538822-150553196	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:150539636-150544211	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr1:150539629-150541828	K562	blood:	n/a	n/a
26	FOS	chr1:150541646-150542861	MCF10A-Er-Src	breast:	n/a	n/a
27	MTA3	chr1:150539001-150541829	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:150538740-150553070	K562	blood:	n/a	n/a
29	POLR2A	chr1:150538874-150549135	GM12878	blood:	n/a	n/a
30	MYC	chr1:150541722-150543456	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr1:150538937-150546714	GM12892	blood:	n/a	n/a
32	POLR2A	chr1:150538892-150546716	GM12892	blood:	n/a	n/a
33	POLR2A	chr1:150539018-150541819	GM12892	blood:	n/a	n/a
34	POLR2A	chr1:150538916-150552586	K562	blood:	n/a	n/a
35	POLR2A	chr1:150540034-150541957	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:150539734-150546272	HUVEC	blood vessel:	n/a	n/a
37	JUND	chr1:150541715-150541847	K562	blood:	n/a	n/a
38	POLR2A	chr1:150541445-150541994	HepG2	liver:	n/a	n/a
39	POLR2A	chr1:150531141-150552175	A549	lung:	n/a	n/a
40	POLR2A	chr1:150541798-150544263	U87	brain:	n/a	n/a
41	POLR2A	chr1:150539585-150552519	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:150539573-150541837	GM12891	blood:	n/a	n/a
43	POLR2A	chr1:150539687-150541877	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr1:150540039-150541867	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr1:150540685-150542908	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:150539635-150541837	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr1:150538971-150546680	GM12892	blood:	n/a	n/a
48	POLR2A	chr1:150539193-150546603	GM18505	blood:	n/a	n/a
49	POLR2A	chr1:150538853-150541886	GM12891	blood:	n/a	n/a
50	FOS	chr1:150541713-150542583	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150541646..150543170-chr22:29209298..29211232,2	MCF-7	breast:
2	chr1:150541068..150543628-chr1:150783525..150786883,3	MCF-7	breast:
3	chr1:150541344..150544160-chr1:150572544..150574410,2	K562	blood:
4	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
5	chr1:150539815..150542556-chr1:150853753..150855583,2	K562	blood:
6	chr1:150539334..150542207-chr1:150782861..150785483,3	K562	blood:
7	chr1:150540144..150542642-chr1:151226920..151228835,2	MCF-7	breast:
8	chr1:150541549..150544184-chr1:150897269..150900025,2	K562	blood:
9	chr1:150539334..150542207-chr1:150782861..150785483,4	K562	blood:

No data

Variant related genes	Relation type
RN7SL600P	TF binding region
RN7SL473P	TF binding region
ENSG00000212512	Chromatin interaction
ENSG00000253047	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000272858	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000224800	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs11204666	0.85[ASN][1000 genomes]
rs11204671	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35967040	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587756	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6655975	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681426	0.81[ASN][1000 genomes]
rs6695123	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv527379	chr1:150527354-150542128	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
4	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7549723	HORMAD1	cis	Esophagus Mucosa	GTEx
rs7549723	HORMAD1	cis	Nerve Tibial	GTEx
rs7549723	RP11-316M1.12	cis	Artery Tibial	GTEx
rs7549723	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs7549723	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs7549723	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs7549723	CTSS	cis	Thyroid	GTEx
rs7549723	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs7549723	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs7549723	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs7549723	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs7549723	RP11-316M1.12	cis	Thyroid	GTEx
rs7549723	RP11-316M1.12	cis	Whole Blood	GTEx
rs7549723	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs7549723	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs7549723	GOLPH3L	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150534400-150547200	Weak transcription	Ovary	ovary
2	chr1:150534600-150542600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:150534600-150542600	Enhancers	Lung	lung
4	chr1:150535000-150542200	Enhancers	Placenta	Placenta
5	chr1:150538800-150543800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:150538800-150543800	Enhancers	HMEC	breast
7	chr1:150539000-150542000	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr1:150539000-150542400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr1:150539000-150543000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:150539200-150542000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:150539200-150542600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:150539200-150542800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr1:150539400-150542200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr1:150539800-150543400	Weak transcription	Gastric	stomach
15	chr1:150540000-150542800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:150540200-150543200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:150540400-150542200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:150540600-150542200	Enhancers	Spleen	Spleen
19	chr1:150540600-150542400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr1:150540600-150542800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:150540600-150543000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:150540600-150543400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
23	chr1:150540600-150543600	Enhancers	Pancreas	Pancrea
24	chr1:150540600-150544200	Enhancers	NHLF	lung
25	chr1:150540600-150544800	Enhancers	Psoas Muscle	Psoas
26	chr1:150540800-150542200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:150540800-150542200	Enhancers	Fetal Intestine Large	intestine
28	chr1:150540800-150542400	Enhancers	Fetal Stomach	stomach
29	chr1:150540800-150542400	Enhancers	Fetal Thymus	thymus
30	chr1:150540800-150542600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:150540800-150543400	Enhancers	Colonic Mucosa	Colon
32	chr1:150540800-150543600	Enhancers	HUVEC	blood vessel
33	chr1:150540800-150543800	Enhancers	NHDF-Ad	bronchial
34	chr1:150540800-150545600	Enhancers	Right Atrium	heart
35	chr1:150540800-150545600	Enhancers	Right Ventricle	heart
36	chr1:150541000-150542000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr1:150541000-150542000	Enhancers	Primary B cells from peripheral blood	blood
38	chr1:150541000-150542000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
39	chr1:150541000-150542200	Enhancers	Thymus	Thymus
40	chr1:150541000-150542400	Enhancers	Fetal Muscle Leg	muscle
41	chr1:150541000-150542800	Enhancers	K562	blood
42	chr1:150541000-150543200	Enhancers	Left Ventricle	heart
43	chr1:150541000-150543400	Enhancers	Brain Hippocampus Middle	brain
44	chr1:150541200-150542000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:150541200-150542200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:150541200-150542400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:150541200-150542400	Enhancers	Stomach Mucosa	stomach
48	chr1:150541200-150542800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:150541200-150542800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:150541200-150543000	Enhancers	H1 Cell Line	embryonic stem cell

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