Variant report

Variant	rs6091737
Chromosome Location	chr20:52349892-52349893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52349507..52351793-chr6:132662386..132665362,2	MCF-7	breast:
2	chr20:45988261..45989864-chr20:52347427..52350014,2	MCF-7	breast:
3	chr12:53773971..53776932-chr20:52348408..52351125,2	MCF-7	breast:
4	chr17:59475494..59478044-chr20:52349419..52353533,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121068	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000185591	Chromatin interaction
ENSG00000267131	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12479726	0.92[ASN][1000 genomes]
rs12480103	0.94[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.89[AMR][1000 genomes]
rs2870276	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55993902	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6022697	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6022698	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6097549	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6097552	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6097553	0.81[ASN][1000 genomes]
rs6126927	0.83[CEU][hapmap]
rs62206459	0.89[AMR][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	nsv1055342	chr20:52126973-52352323	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	214 gene(s)	inside rSNPs	diseases
2	esv3412883	chr20:52176349-52393416	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
3	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
4	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Calcium levels	20705733	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6091737	TSHZ2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52331200-52352600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52341800-52354800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:52342000-52352200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr20:52346400-52351600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr20:52346400-52352800	Weak transcription	Spleen	Spleen
6	chr20:52346600-52350400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr20:52346600-52350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr20:52346800-52352000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:52347200-52350400	Weak transcription	HepG2	liver
10	chr20:52347200-52352000	Weak transcription	Fetal Thymus	thymus
11	chr20:52347200-52352200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr20:52347200-52352400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr20:52347200-52352800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr20:52347200-52353400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr20:52347400-52350800	Weak transcription	GM12878-XiMat	blood
16	chr20:52347600-52350600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr20:52347600-52352000	Weak transcription	Primary B cells from cord blood	blood
18	chr20:52347600-52352000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr20:52348200-52350200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr20:52348200-52350600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr20:52348600-52350600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr20:52348600-52357600	Enhancers	Placenta	Placenta
23	chr20:52349800-52350000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr20:52349800-52350000	Enhancers	Brain Cingulate Gyrus	brain
25	chr20:52349800-52350200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:52349800-52351600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr20:52349800-52351800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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