Variant report

Variant	rs7668240
Chromosome Location	chr4:79559423-79559424
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	RELA	chr4:79558885-79560367	GM18951	blood:	n/a	n/a
2	MTA3	chr4:79559400-79560150	GM12878	blood:	n/a	n/a
3	EP300	chr4:79558934-79560251	GM12878	blood:	n/a	chr4:79560125-79560139 chr4:79560020-79560034
4	RELA	chr4:79558837-79560320	GM10847	blood:	n/a	n/a
5	SPI1	chr4:79559330-79559588	GM12891	blood:	n/a	n/a
6	ATF2	chr4:79559350-79560346	GM12878	blood:	n/a	n/a
7	SPI1	chr4:79559293-79559561	GM12878	blood:	n/a	n/a
8	RELA	chr4:79558875-79560385	GM12891	blood:	n/a	n/a
9	RELA	chr4:79558877-79560347	GM19099	blood:	n/a	n/a
10	NFIC	chr4:79559392-79560273	GM12878	blood:	n/a	n/a
11	MTA3	chr4:79559408-79560332	GM12878	blood:	n/a	n/a
12	SPI1	chr4:79559366-79559500	K562	blood:	n/a	n/a
13	EP300	chr4:79559334-79560248	GM12878	blood:	n/a	chr4:79560125-79560139 chr4:79560020-79560034
14	RELA	chr4:79558843-79560361	GM12878	blood:	n/a	n/a
15	SPI1	chr4:79559294-79559667	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79557761..79562686-chr4:79563110..79568703,4	K562	blood:
2	chr4:79557978..79560128-chr4:79697718..79699238,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238816	TF binding region
ENSG00000251442	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1042515	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11727844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11729862	0.87[JPT][hapmap]
rs12640075	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12641789	0.84[AMR][1000 genomes]
rs17003396	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35628566	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4382063	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs56023152	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57415147	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57896096	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59133103	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5950	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67280698	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6817792	0.85[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6819559	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6836185	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6837823	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72607862	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72607863	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72607864	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72607865	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72607866	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7661370	0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7668240	RP11-792D21.2	cis	Whole Blood	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79549600-79560000	Weak transcription	HMEC	breast
2	chr4:79550400-79564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:79551400-79578200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:79553000-79561600	Weak transcription	Placenta	Placenta
5	chr4:79553200-79563000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:79554000-79561600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:79555400-79562000	Weak transcription	Brain Substantia Nigra	brain
8	chr4:79555600-79564000	Weak transcription	Fetal Intestine Large	intestine
9	chr4:79555800-79566400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:79556000-79564000	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:79557200-79568000	Enhancers	Primary B cells from cord blood	blood
12	chr4:79558400-79559800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr4:79558400-79560800	Enhancers	Primary hematopoietic stem cells	blood
14	chr4:79558400-79561000	Enhancers	Primary B cells from peripheral blood	blood
15	chr4:79558600-79559600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:79558800-79560200	Enhancers	Primary T cells from cord blood	blood
17	chr4:79558800-79560200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr4:79558800-79561200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:79559000-79560400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr4:79559000-79560400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:79559200-79559600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:79559200-79560400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr4:79559200-79560400	Flanking Active TSS	GM12878-XiMat	blood
24	chr4:79559400-79559600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr4:79559400-79560000	Enhancers	Duodenum Mucosa	Duodenum
26	chr4:79559400-79560200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr4:79559400-79560400	Enhancers	Dnd41	blood
28	chr4:79559400-79561000	Enhancers	Fetal Thymus	thymus
29	chr4:79559400-79561000	Enhancers	K562	blood
30	chr4:79559400-79561000	Enhancers	NHEK	skin

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