Variant report

Variant	rs9370542
Chromosome Location	chr6:56467224-56467225
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	CTCF	chr6:56467193-56467226	GM20000	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56465447..56467405-chr6:56469349..56471990,2	MCF-7	breast:

Variant related genes	Relation type
DST	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1014309	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1014310	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10456736	0.86[EUR][1000 genomes]
rs10484858	0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10807515	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10949003	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11751914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11969402	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12195236	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12200301	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12201550	0.86[EUR][1000 genomes]
rs13194995	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13197391	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13209548	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1474853	0.84[EUR][1000 genomes]
rs1474854	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16888055	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884284	0.96[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1884285	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1884286	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2024751	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2067543	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2144405	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2230862	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28759439	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36017808	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4712135	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4712136	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712137	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4712138	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715635	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6459166	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6919941	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6920543	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6921099	0.83[EUR][1000 genomes]
rs6926648	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6929091	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6931836	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7747060	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7759479	0.89[YRI][hapmap]
rs7760503	0.89[YRI][hapmap]
rs7772239	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9349829	0.87[EUR][1000 genomes]
rs9349830	0.84[EUR][1000 genomes]
rs9349831	0.87[EUR][1000 genomes]
rs9349832	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9349834	0.82[AMR][1000 genomes]
rs9349835	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9349836	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9357923	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs9357924	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9357927	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9367689	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9367690	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs9370538	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9370539	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9370540	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9370541	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370543	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370544	0.84[ASN][1000 genomes]
rs9382650	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9382652	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9382653	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382654	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382655	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382656	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9382658	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382659	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9396221	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9396222	0.80[ASN][1000 genomes]
rs9396224	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9396225	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9396228	0.90[EUR][1000 genomes]
rs9475721	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9475722	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9475723	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9475724	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9689355	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9370542	BEND6	cis	cerebellum	SCAN
rs9370542	BARD1	trans	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
3	chr6:56417200-56481400	Weak transcription	Esophagus	oesophagus
4	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine
5	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
6	chr6:56451800-56514200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:56452200-56514600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:56452800-56469200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:56452800-56470000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:56452800-56476000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:56452800-56489400	Strong transcription	Liver	Liver
12	chr6:56453000-56468800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:56453000-56469000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:56453000-56469000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:56453000-56469200	Strong transcription	Fetal Intestine Large	intestine
16	chr6:56453000-56469800	Strong transcription	NH-A	brain
17	chr6:56453000-56492000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:56453000-56502200	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr6:56453000-56506800	Strong transcription	HSMM	muscle
20	chr6:56453200-56470000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:56453400-56469200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:56453400-56476200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:56453800-56469000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:56453800-56470800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:56454200-56467400	Strong transcription	HMEC	breast
26	chr6:56455400-56476000	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:56455400-56486200	Strong transcription	HSMMtube	muscle
28	chr6:56457000-56468000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:56457000-56468000	Weak transcription	Psoas Muscle	Psoas
30	chr6:56457200-56473200	Weak transcription	Aorta	Aorta
31	chr6:56457200-56478200	Weak transcription	Fetal Heart	heart
32	chr6:56457200-56501200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:56458800-56488200	Weak transcription	HepG2	liver
34	chr6:56459000-56496200	Weak transcription	Fetal Kidney	kidney
35	chr6:56459000-56502400	Strong transcription	Osteobl	bone
36	chr6:56459000-56521000	Weak transcription	Spleen	Spleen
37	chr6:56459200-56468800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:56459200-56473000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:56459800-56479200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr6:56460000-56469400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:56460000-56471600	Weak transcription	Ovary	ovary
42	chr6:56460400-56469000	Strong transcription	Brain Anterior Caudate	brain
43	chr6:56460600-56496000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr6:56460600-56513600	Weak transcription	Stomach Mucosa	stomach
45	chr6:56460800-56476800	Strong transcription	NHDF-Ad	bronchial
46	chr6:56460800-56489000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr6:56461200-56468800	Strong transcription	Adipose Nuclei	Adipose
48	chr6:56461200-56468800	Strong transcription	Brain Substantia Nigra	brain
49	chr6:56461200-56468800	Strong transcription	GM12878-XiMat	blood
50	chr6:56461200-56469000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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