Variant report

Variant	rs4397225
Chromosome Location	chr6:53706237-53706238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53672081..53674984-chr6:53705343..53707160,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10498795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543356	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs16884427	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17748452	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2223617	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2473599	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2473603	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2494087	0.84[AMR][1000 genomes]
rs2494090	0.82[AMR][1000 genomes]
rs2820217	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2820218	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3000998	0.85[CHB][hapmap]
rs3799261	1.00[JPT][hapmap]
rs4077760	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs4131378	0.83[EUR][1000 genomes]
rs4272222	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4276504	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4357137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4380749	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4476827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580851	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908101	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6919924	0.86[EUR][1000 genomes]
rs6925165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761135	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs7752696	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464005	0.80[AMR][1000 genomes]
rs9474672	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4397225	FBXO9	cis	parietal	SCAN
rs4397225	COL21A1	cis	cerebellum	SCAN
rs4397225	C6orf142	cis	cerebellum	SCAN
rs4397225	TFAP2D	cis	cerebellum	SCAN
rs4397225	LRRC1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
4	chr6:53694000-53708400	Weak transcription	Fetal Thymus	thymus
5	chr6:53695000-53710000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:53696400-53708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:53699400-53709200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:53700400-53709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:53703000-53708600	Weak transcription	Gastric	stomach
14	chr6:53703000-53718600	Weak transcription	Pancreas	Pancrea
15	chr6:53703200-53710400	Weak transcription	HUVEC	blood vessel
16	chr6:53703200-53720000	Weak transcription	HSMMtube	muscle
17	chr6:53703200-53720200	Weak transcription	Aorta	Aorta
18	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
19	chr6:53703400-53707400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:53703400-53710200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:53703600-53710600	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:53703800-53717200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:53704000-53708600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:53704400-53707400	Weak transcription	Brain Angular Gyrus	brain
26	chr6:53704400-53710600	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:53704600-53710800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:53704800-53711600	Weak transcription	Brain Germinal Matrix	brain
29	chr6:53705400-53708000	Weak transcription	HepG2	liver
30	chr6:53705400-53718800	Weak transcription	NHEK	skin
31	chr6:53705600-53707400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:53705800-53706400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr6:53706000-53708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:53706000-53708600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:53706000-53708600	Weak transcription	Thymus	Thymus
36	chr6:53706000-53709400	Weak transcription	Primary B cells from cord blood	blood
37	chr6:53706000-53709400	Weak transcription	Fetal Intestine Small	intestine
38	chr6:53706000-53710400	Weak transcription	Brain Substantia Nigra	brain
39	chr6:53706000-53720200	Weak transcription	Esophagus	oesophagus
40	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:53706200-53712200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell

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