Variant report

Variant	rs7006402
Chromosome Location	chr8:10183347-10183348
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	NFIC	chr8:10183232-10183954	GM12878	blood:	n/a	n/a
2	BATF	chr8:10183330-10183659	GM12878	blood:	n/a	chr8:10183510-10183521
3	RUNX3	chr8:10183098-10184103	GM12878	blood:	n/a	n/a
4	NR2F2	chr8:10183061-10183375	MCF-7	breast:	n/a	n/a
5	GATA3	chr8:10182877-10183398	MCF-7	breast:	n/a	chr8:10183168-10183184 chr8:10183172-10183181

Variant related genes	Relation type
MSRA	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10105033	0.88[ASN][1000 genomes]
rs10105815	0.91[MEX][hapmap];0.85[AMR][1000 genomes]
rs10903323	0.91[MEX][hapmap];0.86[AMR][1000 genomes]
rs11249982	0.87[AMR][1000 genomes]
rs11249983	0.87[AMR][1000 genomes]
rs11249986	0.81[CHB][hapmap]
rs11249987	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11249988	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap]
rs11249989	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11775021	0.88[ASN][1000 genomes]
rs12676847	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13250850	0.92[ASN][1000 genomes]
rs13251198	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs17151700	0.81[AMR][1000 genomes]
rs17151731	0.81[CHB][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs17151759	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2003225	0.89[ASN][1000 genomes]
rs2003226	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34113732	0.88[ASN][1000 genomes]
rs35965591	0.93[ASN][1000 genomes]
rs36089236	0.86[AMR][1000 genomes]
rs4240642	0.86[AMR][1000 genomes]
rs4278158	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4307347	0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs4329276	0.81[CHB][hapmap]
rs4335130	0.81[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.82[YRI][hapmap]
rs4419814	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4498602	0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4509385	0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4546664	0.81[CHB][hapmap]
rs4577961	0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7818111	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7821327	0.91[MEX][hapmap];0.85[AMR][1000 genomes]
rs7825984	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9644722	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1016347	chr8:10091475-10223667	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv890347	chr8:10153082-10331636	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7006402	MFHAS1	cis	cerebellum	SCAN
rs7006402	TDH	cis	cerebellum	SCAN
rs7006402	FLJ10661	cis	cerebellum	SCAN
rs7006402	DEFB134	cis	cerebellum	SCAN
rs7006402	BLK	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10168400-10188600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr8:10169000-10183600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr8:10176600-10191200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:10178600-10190400	Weak transcription	Primary B cells from cord blood	blood
5	chr8:10179400-10183400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr8:10179400-10183600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:10179400-10188400	Weak transcription	Brain Hippocampus Middle	brain
8	chr8:10179400-10189600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr8:10179400-10189800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr8:10179400-10190000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr8:10179400-10190000	Weak transcription	Brain Substantia Nigra	brain
12	chr8:10179400-10190400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr8:10179400-10190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr8:10179400-10191200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr8:10179400-10191200	Weak transcription	Fetal Intestine Small	intestine
16	chr8:10179400-10191200	Weak transcription	Pancreas	Pancrea
17	chr8:10179400-10192000	Weak transcription	Aorta	Aorta
18	chr8:10179600-10188000	Weak transcription	Fetal Brain Female	brain
19	chr8:10179600-10188400	Weak transcription	Brain Anterior Caudate	brain
20	chr8:10179600-10190200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr8:10179800-10183600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr8:10180200-10183400	Weak transcription	Brain Germinal Matrix	brain
23	chr8:10180200-10190200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr8:10180400-10183400	Weak transcription	Primary T cells from cord blood	blood
25	chr8:10182400-10183800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr8:10182600-10190600	Weak transcription	Spleen	Spleen
27	chr8:10182600-10192000	Weak transcription	Right Ventricle	heart
28	chr8:10182800-10186800	Weak transcription	Fetal Brain Male	brain
29	chr8:10183000-10184600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr8:10183000-10185000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr8:10183200-10183600	Enhancers	GM12878-XiMat	blood
32	chr8:10183200-10184000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr8:10183200-10184000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr8:10183200-10184000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr8:10183200-10184000	Enhancers	Brain Angular Gyrus	brain
36	chr8:10183200-10184400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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