Variant report

Variant	rs4283986
Chromosome Location	chr7:128348741-128348742
allele	A/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	JUND	chr7:128348248-128349208	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF143	chr7:128348714-128349121	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:128348727-128349494	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:128346237..128350299-chr7:128378242..128382310,4	K562	blood:
2	chr7:128346113..128353140-chr7:128377714..128381349,8	K562	blood:

Variant related genes	Relation type
FAM71F1	TF binding region
ENSG00000128595	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10276394	0.87[ASN][1000 genomes]
rs10954193	0.89[LWK][hapmap]
rs1109552	0.89[LWK][hapmap]
rs11973846	0.89[MKK][hapmap];0.88[TSI][hapmap]
rs12674125	0.89[LWK][hapmap]
rs1450874	0.89[LWK][hapmap]
rs17169024	0.86[LWK][hapmap]
rs339078	0.80[CHD][hapmap]
rs3807125	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3807126	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4307280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs4524716	0.82[ASN][1000 genomes]
rs4554406	0.89[LWK][hapmap]
rs4728130	0.89[LWK][hapmap]
rs4731507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][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]
rs6467210	0.89[LWK][hapmap]
rs6946321	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6958788	0.89[LWK][hapmap]
rs72607753	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7793136	0.86[LWK][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4283986	TMEM209	cis	parietal	SCAN
rs4283986	KLHDC10	cis	parietal	SCAN
rs4283986	LRRC4	cis	cerebellum	SCAN
rs4283986	OPN1SW	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128338600-128349000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:128339000-128358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:128344000-128349000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:128345200-128350200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:128345200-128350200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:128345400-128348800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:128346000-128349000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:128346200-128350400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr7:128346400-128350200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:128346400-128350200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr7:128346400-128350200	Weak transcription	NHEK	skin
12	chr7:128346400-128353400	Weak transcription	HMEC	breast
13	chr7:128346400-128354000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:128346600-128353400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:128348200-128349800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:128348400-128348800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr7:128348400-128349600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr7:128348600-128349000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr7:128348600-128349000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr7:128348600-128349400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr7:128348600-128349400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:128348600-128349400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr7:128348600-128349400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr7:128348600-128349400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr7:128348600-128349600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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