Variant report

Variant	rs7620848
Chromosome Location	chr3:49828021-49828022
allele	C/G
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	chr3:49827313-49828066	H1-neurons	neurons:	n/a	n/a
2	REST	chr3:49827146-49828452	H1-neurons	neurons:	n/a	chr3:49828347-49828360
3	POLR2A	chr3:49827354-49828135	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49822510..49825431-chr3:49825624..49828920,3	MCF-7	breast:
2	chr3:49822569..49826385-chr3:49827149..49830694,4	MCF-7	breast:

Variant related genes	Relation type
IP6K1	TF binding region
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1078341	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11130211	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs11130217	0.92[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720705	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12637313	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs12715437	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13096480	1.00[YRI][hapmap]
rs13097720	1.00[ASN][1000 genomes]
rs1352889	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs1491983	0.92[CEU][hapmap];0.87[YRI][hapmap]
rs1491985	1.00[CEU][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1586827	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17304079	1.00[ASN][1000 genomes]
rs1799844	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996663	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1996664	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2029591	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2131108	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2329021	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs28535523	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375092	1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	1.00[ASN][1000 genomes]
rs4241405	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs4855833	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs4855845	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4855846	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4855882	1.00[CEU][hapmap]
rs4855885	1.00[CEU][hapmap]
rs55924524	1.00[ASN][1000 genomes]
rs55997059	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58339610	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357103	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59684465	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61557789	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62260663	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260723	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62262722	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs6787892	1.00[ASN][1000 genomes]
rs6790568	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804970	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809879	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs71326915	1.00[ASN][1000 genomes]
rs7613603	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7621797	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628207	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7637711	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649428	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap]
rs9829155	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830730	1.00[CEU][hapmap]
rs9835157	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836756	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849038	1.00[CEU][hapmap]
rs9851651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883000	1.00[CEU][hapmap];1.00[YRI][hapmap]

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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7620848	RNF123	cis	Artery Tibial	GTEx
rs7620848	AMT	cis	lung	GTEx
rs7620848	AMT	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49824600-49828200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49824600-49829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:49824600-49832400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49824800-49828200	Weak transcription	NH-A	brain
5	chr3:49824800-49832600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:49825200-49828400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:49825200-49836400	Weak transcription	Esophagus	oesophagus
8	chr3:49825400-49828400	Weak transcription	K562	blood
9	chr3:49825600-49840000	Weak transcription	Spleen	Spleen
10	chr3:49827200-49828200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:49827200-49828200	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:49827200-49828200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:49827200-49828400	Enhancers	Fetal Thymus	thymus
14	chr3:49827200-49828600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:49827200-49828800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:49827200-49829000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:49827400-49828400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:49827400-49828600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:49827400-49828800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:49827400-49829000	Enhancers	HepG2	liver
21	chr3:49827400-49829600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:49827600-49828200	Enhancers	HUVEC	blood vessel
23	chr3:49827600-49828800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:49827800-49828400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:49827800-49828600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:49827800-49829200	Enhancers	Placenta Amnion	Placenta Amnion

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