Variant report

Variant	rs6854896
Chromosome Location	chr4:90871561-90871562
allele	C/T
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	RAD21	chr4:90870881-90871591	SK-N-SH	brain:	n/a	chr4:90871119-90871138

Variant related genes	Relation type
MMRN1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10516858	0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs1117840	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1117841	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11933698	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11939062	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11939159	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11941275	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12643741	0.87[ASN][1000 genomes]
rs12651123	0.83[CHB][hapmap]
rs13124183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13126339	0.87[ASN][1000 genomes]
rs13131903	0.85[ASN][1000 genomes]
rs13143093	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1318557	0.98[ASN][1000 genomes]
rs1318558	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1443799	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479427	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479429	0.90[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479430	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17195014	0.83[ASN][1000 genomes]
rs17808829	0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2120375	0.85[ASN][1000 genomes]
rs34997679	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35817029	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822098	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62312682	0.95[ASN][1000 genomes]
rs62312688	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62312690	0.87[ASN][1000 genomes]
rs6830014	0.86[CHB][hapmap]
rs723992	0.81[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs7662354	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7667606	0.98[ASN][1000 genomes]
rs920805	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs992612	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv997700	chr4:90791866-90920021	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830005	chr4:90799398-90963420	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1003903	chr4:90831805-90947922	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1011876	chr4:90851535-90952723	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv998230	chr4:90854555-90952723	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv999030	chr4:90859531-90952723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv432616	chr4:90862943-90952424	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv516189	chr4:90866819-90952424	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv594821	chr4:90871561-90962886	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6854896	FAM190A	cis	cerebellum	SCAN
rs6854896	MMRN1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90855000-90872400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr4:90856800-90878200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:90859200-90872600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:90861400-90872400	Weak transcription	HUVEC	blood vessel
5	chr4:90867400-90872400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:90868400-90875600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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