Variant report

Variant	rs10497971
Chromosome Location	chr2:213224859-213224860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:213213790..213216008-chr2:213223245..213225984,2	MCF-7	breast:
2	chr2:213217638..213221383-chr2:213223310..213226579,3	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10165393	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10176489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186360	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10186462	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10186519	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10186681	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10189506	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10201724	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10205953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10211056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682488	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12104818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12104831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694278	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12994366	0.93[ASN][1000 genomes]
rs12994616	1.00[JPT][hapmap]
rs12998688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13004266	1.00[JPT][hapmap]
rs13014726	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13015805	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.81[TSI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13016456	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs13016554	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13027907	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13031888	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13034566	1.00[JPT][hapmap]
rs13034755	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs1394800	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1505351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1505352	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1505375	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16848535	1.00[JPT][hapmap]
rs16848540	1.00[JPT][hapmap]
rs1876047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2013073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510380	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34623832	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34777887	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4465721	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4627509	1.00[ASW][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap]
rs62184103	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6738011	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006051	chr2:213052804-213273642	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv584346	chr2:213067749-213258622	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv834526	chr2:213114901-213237146	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv834527	chr2:213115966-213334308	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1014680	chr2:213142147-213301614	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1004573	chr2:213186537-213365252	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv875811	chr2:213200920-213347104	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv3149	chr2:213204282-213248966	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv584422	chr2:213214303-213270427	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1003694	chr2:213216431-213290523	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10497971	PTH2R	cis	cerebellum	SCAN
rs10497971	RPE	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213219200-213227200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:213219200-213233600	Weak transcription	Psoas Muscle	Psoas
3	chr2:213221000-213228600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:213224000-213225200	Enhancers	Fetal Intestine Small	intestine
5	chr2:213224000-213225400	Enhancers	Fetal Intestine Large	intestine
6	chr2:213224000-213227200	Enhancers	Fetal Heart	heart
7	chr2:213224200-213225200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:213224200-213225200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:213224200-213225400	Enhancers	Brain Angular Gyrus	brain
10	chr2:213224200-213225400	Enhancers	Brain Hippocampus Middle	brain
11	chr2:213224200-213225400	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr2:213224200-213226400	Enhancers	Brain Substantia Nigra	brain
13	chr2:213224200-213227400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:213224400-213225000	Active TSS	Aorta	Aorta
15	chr2:213224400-213225200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:213224400-213225200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr2:213224600-213225000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:213224600-213225200	Enhancers	Fetal Kidney	kidney
19	chr2:213224600-213225200	Flanking Active TSS	HepG2	liver
20	chr2:213224600-213226400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:213224600-213228800	Weak transcription	Brain Germinal Matrix	brain
22	chr2:213224800-213225000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr2:213224800-213225000	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr2:213224800-213225200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:213224800-213225400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:213224800-213225400	Flanking Active TSS	Brain Anterior Caudate	brain

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