Variant report

Variant	rs1011665
Chromosome Location	chr6:27332298-27332299
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	chr6:27331082..27332744-chr6:27341177..27342720,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124613	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10946915	0.93[ASN][1000 genomes]
rs12526495	0.86[ASN][1000 genomes]
rs12529458	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12663650	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12664996	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13220817	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1883403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064093	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs2206250	0.83[CHD][hapmap]
rs2235232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2393926	0.97[ASN][1000 genomes]
rs2393962	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs2393964	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs4711152	0.90[ASN][1000 genomes]
rs4713098	0.82[ASN][1000 genomes]
rs4713099	0.82[ASN][1000 genomes]
rs6901629	0.81[AFR][1000 genomes]
rs6913166	0.83[ASW][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914864	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6922815	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71559025	0.82[ASN][1000 genomes]
rs764284	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7761966	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs7772739	0.97[ASN][1000 genomes]
rs9357038	0.92[ASN][1000 genomes]
rs9379980	0.86[ASN][1000 genomes]
rs9393813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1011665	ZNF391	cis	lung	GTEx
rs1011665	HIST1H3B	cis	cerebellum	SCAN
rs1011665	ZNF391	cis	Thyroid	GTEx
rs1011665	ZSCAN23	cis	cerebellum	SCAN
rs1011665	ZNF204P	cis	parietal	SCAN
rs1011665	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx
rs1011665	ZNF204P	cis	cerebellum	SCAN
rs1011665	ZNF391	cis	Artery Tibial	GTEx
rs1011665	ZNF391	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27316800-27335400	Weak transcription	Pancreas	Pancrea
2	chr6:27325800-27336200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:27326000-27335600	Weak transcription	Brain Germinal Matrix	brain
4	chr6:27326800-27342000	Weak transcription	Colonic Mucosa	Colon
5	chr6:27327000-27342000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:27327400-27333400	Weak transcription	Aorta	Aorta
7	chr6:27327400-27335600	Weak transcription	Gastric	stomach
8	chr6:27327400-27335800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:27327400-27336600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:27327400-27341800	Weak transcription	Fetal Brain Male	brain
11	chr6:27327400-27341800	Weak transcription	Fetal Kidney	kidney
12	chr6:27327600-27335800	Weak transcription	Brain Angular Gyrus	brain
13	chr6:27327600-27342200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:27328000-27335600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:27328000-27342400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:27328200-27335800	Weak transcription	Right Ventricle	heart
17	chr6:27328200-27341800	Weak transcription	Adipose Nuclei	Adipose
18	chr6:27328200-27341800	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:27328200-27341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:27328200-27342200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:27328400-27335200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:27328400-27341800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:27329200-27335600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:27329400-27335400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:27329400-27337000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:27329400-27341800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:27329600-27335600	Weak transcription	Lung	lung
28	chr6:27329800-27335000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:27329800-27335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:27329800-27335600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:27329800-27342000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:27330200-27335600	Weak transcription	Fetal Stomach	stomach
33	chr6:27330200-27341400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:27330600-27335600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:27330600-27341800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:27330600-27341800	Weak transcription	Brain Anterior Caudate	brain
37	chr6:27331200-27333600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:27331200-27335600	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:27331200-27335600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:27331200-27335600	Weak transcription	Fetal Lung	lung
41	chr6:27331200-27335800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:27331200-27341600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:27331200-27341800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:27331400-27335400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:27331600-27335200	Weak transcription	Ovary	ovary
46	chr6:27331600-27342000	Weak transcription	Left Ventricle	heart
47	chr6:27332200-27332600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr6:27332200-27332600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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