Variant report

Variant	rs2472559
Chromosome Location	chr7:100398929-100398930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100397602..100400701-chr7:100463171..100467271,4	K562	blood:
2	chr7:100398509..100403276-chr7:100410135..100416305,9	MCF-7	breast:
3	chr7:100398318..100400624-chr7:100418160..100420117,2	K562	blood:
4	chr7:100397131..100401611-chr7:100484722..100488354,5	MCF-7	breast:
5	chr7:100395173..100397781-chr7:100398399..100402175,4	K562	blood:
6	chr7:100026015..100028252-chr7:100398886..100401457,2	K562	blood:
7	chr7:100398521..100399152-chr7:100449312..100450211,3	K562	blood:
8	chr7:100398052..100401560-chr7:100421324..100424929,6	K562	blood:
9	chr7:100398804..100401512-chr7:100476210..100478233,3	MCF-7	breast:
10	chr7:100397305..100400586-chr7:100409020..100412104,3	K562	blood:
11	chr7:100393512..100397050-chr7:100397578..100401575,4	MCF-7	breast:
12	chr7:100303631..100305355-chr7:100397590..100399187,2	MCF-7	breast:
13	chr7:100397181..100400945-chr7:100448287..100452059,6	MCF-7	breast:
14	chr7:100396968..100399232-chr7:100399904..100402635,3	K562	blood:
15	chr7:100368895..100370720-chr7:100398110..100400300,2	K562	blood:
16	chr7:100395722..100403808-chr7:100446660..100452489,13	K562	blood:
17	chr7:100398724..100401678-chr7:100401884..100405733,4	MCF-7	breast:
18	chr7:100319576..100322114-chr7:100397770..100400557,3	MCF-7	breast:
19	chr7:100397084..100399462-chr7:100416639..100419126,2	K562	blood:
20	chr7:100394796..100404152-chr7:100420595..100427156,30	MCF-7	breast:
21	chr7:100397602..100400529-chr7:100463171..100466145,2	K562	blood:
22	chr7:100398877..100402818-chr7:100471202..100474320,4	MCF-7	breast:
23	chr7:100396860..100402994-chr7:100420596..100426493,12	MCF-7	breast:
24	chr7:100395722..100399460-chr7:100448041..100450326,3	K562	blood:
25	chr7:100395512..100400590-chr7:100483994..100490629,8	K562	blood:
26	chr7:100398157..100400014-chr7:100422584..100424999,9	MCF-7	breast:
27	chr7:100398915..100401740-chr7:100464391..100466395,2	MCF-7	breast:
28	chr7:100301814..100305937-chr7:100395370..100399067,4	K562	blood:
29	chr7:100395163..100402625-chr7:100430790..100439308,9	K562	blood:
30	chr7:100388495..100393030-chr7:100395666..100399292,5	MCF-7	breast:
31	chr7:100398676..100402755-chr7:100422988..100426913,7	K562	blood:
32	chr7:100396999..100399481-chr7:100432100..100434547,2	MCF-7	breast:
33	chr7:100394911..100396702-chr7:100397930..100402175,4	K562	blood:
34	chr7:100389809..100393337-chr7:100395699..100399454,7	MCF-7	breast:
35	chr7:100398769..100401112-chr7:100407441..100409562,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236305	Chromatin interaction
ENSG00000146828	Chromatin interaction
ENSG00000087087	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000176125	Chromatin interaction
ENSG00000087077	Chromatin interaction
ENSG00000263672	Chromatin interaction
ENSG00000196411	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs144173	0.93[EUR][1000 genomes]
rs1734903	0.81[EUR][1000 genomes]
rs221804	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2230585	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2406146	0.86[EUR][1000 genomes]
rs3134668	0.81[EUR][1000 genomes]
rs314309	0.87[EUR][1000 genomes]
rs314310	0.87[EUR][1000 genomes]
rs314341	0.92[EUR][1000 genomes]
rs314343	0.95[EUR][1000 genomes]
rs314344	0.93[EUR][1000 genomes]
rs314347	0.95[EUR][1000 genomes]
rs314353	0.90[EUR][1000 genomes]
rs314357	0.90[EUR][1000 genomes]
rs314358	0.89[EUR][1000 genomes]
rs314359	0.93[EUR][1000 genomes]
rs482308	0.82[EUR][1000 genomes]
rs484921	0.81[EUR][1000 genomes]
rs489830	0.81[EUR][1000 genomes]
rs531503	0.82[EUR][1000 genomes]
rs559208	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv888796	chr7:100313420-100423365	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
10	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
11	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
12	esv3478314	chr7:100397058-100399155	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	esv3478315	chr7:100397212-100399055	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2472559	SLC12A9	cis	occipital cortex	BrainEAC

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100382600-100400800	Weak transcription	Right Atrium	heart
2	chr7:100392200-100399600	Weak transcription	NH-A	brain
3	chr7:100392400-100399400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:100392400-100400000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:100392600-100399800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:100392800-100400600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:100393000-100399600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:100393000-100399800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:100393000-100400600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:100393000-100400800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:100394800-100399800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:100396000-100399800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:100396000-100400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:100396000-100400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:100396200-100399400	Enhancers	HepG2	liver
16	chr7:100396200-100400200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr7:100396200-100401800	Enhancers	Primary hematopoietic stem cells	blood
18	chr7:100396400-100399600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:100396800-100399000	Enhancers	HUVEC	blood vessel
20	chr7:100397000-100399400	Enhancers	K562	blood
21	chr7:100397000-100399600	Enhancers	A549	lung
22	chr7:100397000-100399800	Enhancers	Fetal Muscle Trunk	muscle
23	chr7:100397000-100399800	Enhancers	Placenta	Placenta
24	chr7:100397000-100401800	Enhancers	Ovary	ovary
25	chr7:100397200-100399400	Enhancers	NHEK	skin
26	chr7:100397200-100399600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:100397200-100400000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:100397200-100400800	Enhancers	Right Ventricle	heart
29	chr7:100397200-100401400	Enhancers	Placenta Amnion	Placenta Amnion
30	chr7:100397200-100401600	Enhancers	Pancreas	Pancrea
31	chr7:100397400-100399600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:100397400-100399600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:100397400-100399600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr7:100397400-100400000	Weak transcription	Primary B cells from cord blood	blood
35	chr7:100397400-100400400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:100397400-100400600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr7:100397400-100401800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:100397600-100399000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:100397600-100399200	Weak transcription	Fetal Thymus	thymus
40	chr7:100397600-100399400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:100397600-100399400	Weak transcription	HSMM	muscle
42	chr7:100397600-100399400	Weak transcription	NHLF	lung
43	chr7:100397600-100399600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:100397600-100400400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr7:100397600-100402400	Weak transcription	Brain Germinal Matrix	brain
46	chr7:100397800-100399600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:100397800-100400800	Weak transcription	Osteobl	bone
48	chr7:100397800-100401800	Enhancers	Lung	lung
49	chr7:100398000-100399600	Weak transcription	Colonic Mucosa	Colon
50	chr7:100398000-100400600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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