Variant report

Variant	rs9394402
Chromosome Location	chr6:37045549-37045550
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37040469..37042667-chr6:37045350..37047958,2	MCF-7	breast:
2	chr6:37045453..37048349-chr6:37049676..37051329,3	K562	blood:
3	chr6:37027012..37030167-chr6:37045267..37048455,4	K562	blood:
4	chr6:37039829..37042150-chr6:37044091..37047669,4	K562	blood:
5	chr6:37045369..37048087-chr6:37049023..37051325,2	K562	blood:
6	chr6:37043566..37047908-chr6:37051801..37055072,4	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10223714	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1224487	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1224488	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1224491	0.80[ASN][1000 genomes]
rs1228575	0.81[ASN][1000 genomes]
rs1724094	0.80[ASN][1000 genomes]
rs1753301	0.81[ASN][1000 genomes]
rs2025998	0.81[ASN][1000 genomes]
rs2094575	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2149336	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4317401	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs4711482	0.81[ASN][1000 genomes]
rs4711483	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4714034	0.81[CEU][hapmap]
rs6457974	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs6457976	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457978	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6457979	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457980	0.89[CEU][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6924660	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6939869	0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7748291	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7750403	0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7750614	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7750717	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7751821	0.88[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7770544	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7774073	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs831484	0.81[ASN][1000 genomes]
rs831487	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs831489	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs831491	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs831497	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs831500	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs831502	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs913499	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913500	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[ASN][1000 genomes]
rs9296207	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9296208	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366927	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9380637	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9380638	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9394401	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9394403	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462258	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470469	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9394402	C6orf130	cis	parietal	SCAN
rs9394402	PIM1	cis	parietal	SCAN
rs9394402	FGD2	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37040000-37051200	Weak transcription	A549	lung
2	chr6:37041000-37047000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:37041200-37045800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:37042800-37045800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:37042800-37047600	Weak transcription	HepG2	liver
6	chr6:37043000-37047400	Weak transcription	K562	blood
7	chr6:37044800-37045600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr6:37044800-37045600	Enhancers	Fetal Stomach	stomach
9	chr6:37044800-37045800	Enhancers	Fetal Brain Male	brain
10	chr6:37044800-37045800	Enhancers	Right Atrium	heart
11	chr6:37044800-37046000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:37044800-37046400	Enhancers	Adipose Nuclei	Adipose
13	chr6:37044800-37046400	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr6:37044800-37047200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:37044800-37047600	Enhancers	NHDF-Ad	bronchial
16	chr6:37045000-37045600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:37045000-37045600	Enhancers	HMEC	breast
18	chr6:37045000-37045600	Enhancers	NHEK	skin
19	chr6:37045000-37045800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:37045000-37045800	Enhancers	Fetal Intestine Small	intestine
21	chr6:37045000-37046000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr6:37045000-37046000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:37045000-37046200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:37045000-37046400	Enhancers	Placenta	Placenta
25	chr6:37045000-37046400	Enhancers	Ovary	ovary
26	chr6:37045000-37046600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:37045000-37048000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:37045200-37045600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
29	chr6:37045200-37045600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
30	chr6:37045200-37045800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:37045200-37045800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:37045200-37045800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:37045200-37045800	Enhancers	Fetal Intestine Large	intestine
34	chr6:37045200-37045800	Enhancers	Left Ventricle	heart
35	chr6:37045200-37045800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr6:37045200-37046000	Enhancers	Brain Hippocampus Middle	brain
37	chr6:37045200-37046000	Enhancers	Esophagus	oesophagus
38	chr6:37045200-37046000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr6:37045200-37046000	Enhancers	Right Ventricle	heart
40	chr6:37045200-37046200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:37045200-37046200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr6:37045200-37046200	Enhancers	Brain Cingulate Gyrus	brain
43	chr6:37045200-37046800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:37045200-37046800	Enhancers	Colon Smooth Muscle	Colon
45	chr6:37045200-37047000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr6:37045200-37047000	Enhancers	Brain Angular Gyrus	brain
47	chr6:37045200-37047000	Enhancers	HSMMtube	muscle
48	chr6:37045200-37047000	Enhancers	NH-A	brain
49	chr6:37045400-37045600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:37045400-37045600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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