Variant report

Variant	rs9397071
Chromosome Location	chr6:150243614-150243615
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	chr6:149865589..149867401-chr6:150242514..150245357,2	MCF-7	breast:
2	chr6:150217021..150219534-chr6:150242538..150245487,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131013	Chromatin interaction
ENSG00000164520	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10457853	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17079029	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2342773	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4142628	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6557137	0.88[EUR][1000 genomes]
rs6557163	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6904335	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6905778	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6910351	0.90[EUR][1000 genomes]
rs6915465	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6927913	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936944	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72997594	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7745070	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7761734	0.96[EUR][1000 genomes]
rs9322226	0.88[EUR][1000 genomes]
rs9322227	0.88[EUR][1000 genomes]
rs9322230	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9322231	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9371216	0.88[EUR][1000 genomes]
rs9371523	0.92[EUR][1000 genomes]
rs9371539	0.90[EUR][1000 genomes]
rs9371555	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9383569	0.88[EUR][1000 genomes]
rs9383573	0.90[EUR][1000 genomes]
rs9383583	0.92[EUR][1000 genomes]
rs9383916	0.90[EUR][1000 genomes]
rs9383942	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9383943	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9383944	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383945	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9397049	0.88[EUR][1000 genomes]
rs9397053	0.88[EUR][1000 genomes]
rs9397056	0.91[EUR][1000 genomes]
rs9397057	0.90[EUR][1000 genomes]
rs9397060	0.90[EUR][1000 genomes]
rs9397394	0.88[EUR][1000 genomes]
rs9397399	0.90[EUR][1000 genomes]
rs9397419	0.90[EUR][1000 genomes]
rs9397447	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9397449	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9397451	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv970172	chr6:150235248-150244455	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9397071	RAET1E	cis	Nerve Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150241200-150243800	Weak transcription	Aorta	Aorta
2	chr6:150242400-150243800	Enhancers	Spleen	Spleen
3	chr6:150242800-150247800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:150243000-150243800	Bivalent Enhancer	Fetal Intestine Large	intestine
5	chr6:150243000-150243800	Weak transcription	Gastric	stomach
6	chr6:150243400-150243800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:150243400-150243800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:150243400-150243800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:150243400-150243800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
10	chr6:150243400-150243800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:150243400-150243800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
12	chr6:150243400-150243800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr6:150243400-150244000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr6:150243400-150244400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:150243400-150244400	Active TSS	Hela-S3	cervix
16	chr6:150243400-150244800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:150243400-150244800	Flanking Active TSS	HMEC	breast
18	chr6:150243400-150245000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:150243400-150245000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:150243600-150243800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
21	chr6:150243600-150243800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:150243600-150243800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:150243600-150243800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr6:150243600-150243800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:150243600-150243800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
26	chr6:150243600-150243800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:150243600-150243800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
28	chr6:150243600-150243800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
29	chr6:150243600-150243800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
30	chr6:150243600-150243800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:150243600-150243800	Enhancers	Adipose Nuclei	Adipose
32	chr6:150243600-150243800	Enhancers	Liver	Liver
33	chr6:150243600-150243800	Enhancers	Brain Angular Gyrus	brain
34	chr6:150243600-150243800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
35	chr6:150243600-150243800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
36	chr6:150243600-150243800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
37	chr6:150243600-150243800	Bivalent Enhancer	Brain Hippocampus Middle	brain
38	chr6:150243600-150243800	Bivalent Enhancer	Brain Substantia Nigra	brain
39	chr6:150243600-150243800	Enhancers	Colon Smooth Muscle	Colon
40	chr6:150243600-150243800	Enhancers	Esophagus	oesophagus
41	chr6:150243600-150243800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr6:150243600-150243800	Bivalent Enhancer	Fetal Brain Female	brain
43	chr6:150243600-150243800	Bivalent Enhancer	Fetal Intestine Small	intestine
44	chr6:150243600-150243800	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr6:150243600-150243800	Bivalent Enhancer	Placenta	Placenta
46	chr6:150243600-150243800	Bivalent Enhancer	Fetal Stomach	stomach
47	chr6:150243600-150243800	Enhancers	Left Ventricle	heart
48	chr6:150243600-150243800	Enhancers	Lung	lung
49	chr6:150243600-150243800	Enhancers	Ovary	ovary
50	chr6:150243600-150243800	Enhancers	Pancreas	Pancrea

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