Variant report

Variant	rs339070
Chromosome Location	chr7:128364823-128364824
allele	C/T
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:128361867..128364880-chr7:128377679..128379846,3	MCF-7	breast:
2	chr7:128355752..128358740-chr7:128362417..128366090,6	K562	blood:
3	chr7:128362954..128365898-chr7:128384016..128385996,2	MCF-7	breast:
4	chr7:128353684..128356694-chr7:128364624..128368743,3	MCF-7	breast:
5	chr7:128334725..128337091-chr7:128364538..128366706,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALU-2	chr7:128364823-128365021	NONHSAT123248

No data

Variant related genes	Relation type
ENSG00000128595	Chromatin interaction
ENSG00000135248	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10224862	1.00[ASN][1000 genomes]
rs10242806	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10274878	0.90[ASN][1000 genomes]
rs10276810	0.95[ASN][1000 genomes]
rs10954205	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11761312	1.00[ASN][1000 genomes]
rs11768485	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12535238	1.00[ASN][1000 genomes]
rs12536288	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12706858	1.00[ASN][1000 genomes]
rs13233377	1.00[ASN][1000 genomes]
rs13237593	1.00[ASN][1000 genomes]
rs339071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339074	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339079	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs339093	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35825132	0.90[ASN][1000 genomes]
rs3816421	0.89[ASN][1000 genomes]
rs4289745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6467181	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6943737	1.00[ASN][1000 genomes]
rs6946179	1.00[ASN][1000 genomes]
rs6960296	0.89[ASN][1000 genomes]
rs6961754	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6971819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6972787	1.00[ASN][1000 genomes]
rs6976879	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6977126	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71548762	1.00[ASN][1000 genomes]
rs7778731	0.81[ASN][1000 genomes]
rs7787764	0.89[ASN][1000 genomes]
rs7790478	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7794447	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7804472	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7810047	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7811083	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1016979	chr7:128333070-128534438	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs339070	RP11-274B21.10	cis	Thyroid	GTEx
rs339070	CICP14	cis	Nerve Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128349400-128378600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:128349800-128378200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:128349800-128378400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:128361600-128378600	Weak transcription	Right Atrium	heart
5	chr7:128364800-128365600	Enhancers	Primary neutrophils fromperipheralblood	blood

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