Variant report

Variant	rs6725527
Chromosome Location	chr2:209221291-209221292
allele	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	chr2:209221224-209221305	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:209220629..209223614-chr2:209226035..209228837,2	MCF-7	breast:

Variant related genes	Relation type
PTH2R	TF binding region
ENSG00000213081	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10177810	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10190458	0.86[AMR][1000 genomes]
rs11538998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885913	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891163	1.00[ASN][1000 genomes]
rs11895188	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12991283	1.00[ASN][1000 genomes]
rs12998277	1.00[ASN][1000 genomes]
rs13395035	1.00[ASN][1000 genomes]
rs13400356	1.00[ASN][1000 genomes]
rs13407268	0.86[AMR][1000 genomes]
rs17699838	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699982	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17700235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866046	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28418905	1.00[ASN][1000 genomes]
rs28885800	1.00[ASN][1000 genomes]
rs34218846	0.84[AFR][1000 genomes]
rs35217101	1.00[ASN][1000 genomes]
rs35293936	1.00[ASN][1000 genomes]
rs59522113	0.84[AFR][1000 genomes]
rs66826643	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67171462	0.80[EUR][1000 genomes]
rs67202912	0.84[AFR][1000 genomes]
rs67581965	0.84[AFR][1000 genomes]
rs67660353	1.00[ASN][1000 genomes]
rs67965883	1.00[ASN][1000 genomes]
rs73070958	0.84[AFR][1000 genomes]
rs7609093	0.84[AFR][1000 genomes]
rs999890	1.00[ASN][1000 genomes]
rs999891	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv875752	chr2:209141066-209235373	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv437315	chr2:209204714-209249613	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv460055	chr2:209208115-209221935	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv584302	chr2:209208115-209221935	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209147400-209225600	Weak transcription	Stomach Mucosa	stomach
2	chr2:209180600-209224600	Strong transcription	Fetal Thymus	thymus
3	chr2:209182400-209224200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:209185600-209224000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:209188400-209221400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:209188400-209223400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:209188800-209221800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:209188800-209222200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:209188800-209222400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:209188800-209222600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:209188800-209223600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:209188800-209223800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:209188800-209224000	Strong transcription	Primary B cells from cord blood	blood
14	chr2:209188800-209224000	Strong transcription	Primary hematopoietic stem cells	blood
15	chr2:209188800-209224200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:209188800-209224400	Strong transcription	Dnd41	blood
17	chr2:209190600-209224200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:209191200-209224200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr2:209195400-209223800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:209198000-209224600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:209199600-209221800	Weak transcription	Small Intestine	intestine
22	chr2:209200600-209221400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:209205400-209223600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:209206600-209223800	Weak transcription	Psoas Muscle	Psoas
25	chr2:209206600-209224200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:209206600-209225400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:209210600-209221400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:209212000-209223600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:209214200-209221600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:209215000-209225400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:209215200-209223800	Strong transcription	GM12878-XiMat	blood
32	chr2:209215200-209224400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:209215400-209221400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr2:209215400-209222000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:209215400-209224400	Strong transcription	Primary T cells from cord blood	blood
36	chr2:209215800-209222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:209216800-209225000	Weak transcription	Spleen	Spleen
38	chr2:209216800-209226800	Weak transcription	Brain Germinal Matrix	brain
39	chr2:209217000-209223800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:209217000-209224200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:209217000-209225800	Weak transcription	Lung	lung
42	chr2:209217200-209223600	Weak transcription	Fetal Stomach	stomach
43	chr2:209217200-209225000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:209218800-209225400	Weak transcription	Fetal Brain Male	brain
45	chr2:209219200-209221600	Weak transcription	HUVEC	blood vessel
46	chr2:209219400-209225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:209219400-209228000	Weak transcription	Hela-S3	cervix
48	chr2:209219600-209221600	Weak transcription	Brain Substantia Nigra	brain
49	chr2:209220000-209221600	Weak transcription	NHLF	lung
50	chr2:209220000-209227600	Weak transcription	Stomach Smooth Muscle	stomach

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