Variant report

Variant	rs9393813
Chromosome Location	chr6:27331596-27331597
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27322944..27325251-chr6:27328933..27331710,2	K562	blood:
2	chr6:27331082..27332744-chr6:27341177..27342720,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124613	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1011665	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]
rs10946915	0.94[ASN][1000 genomes]
rs12526495	0.86[ASN][1000 genomes]
rs12529458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12663650	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12664996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13220817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1883403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2064093	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2235232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2393926	0.98[ASN][1000 genomes]
rs2393962	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2393964	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4711152	0.90[ASN][1000 genomes]
rs4713098	0.83[ASN][1000 genomes]
rs4713099	0.83[ASN][1000 genomes]
rs6913166	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914864	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6922815	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71559025	0.83[ASN][1000 genomes]
rs764284	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7761966	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7772739	0.98[ASN][1000 genomes]
rs9357038	0.92[ASN][1000 genomes]
rs9379980	0.86[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9393813	ZNF391	cis	Thyroid	GTEx
rs9393813	ZNF391	cis	lung	GTEx
rs9393813	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

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	chr6:27326400-27331800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:27326800-27342000	Weak transcription	Colonic Mucosa	Colon
6	chr6:27327000-27332000	Weak transcription	Stomach Mucosa	stomach
7	chr6:27327000-27342000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:27327400-27333400	Weak transcription	Aorta	Aorta
9	chr6:27327400-27335600	Weak transcription	Gastric	stomach
10	chr6:27327400-27335800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:27327400-27336600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:27327400-27341800	Weak transcription	Fetal Brain Male	brain
13	chr6:27327400-27341800	Weak transcription	Fetal Kidney	kidney
14	chr6:27327600-27335800	Weak transcription	Brain Angular Gyrus	brain
15	chr6:27327600-27342200	Weak transcription	Brain Substantia Nigra	brain
16	chr6:27328000-27335600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:27328000-27342400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:27328200-27335800	Weak transcription	Right Ventricle	heart
19	chr6:27328200-27341800	Weak transcription	Adipose Nuclei	Adipose
20	chr6:27328200-27341800	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:27328200-27341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:27328200-27342200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:27328400-27335200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:27328400-27341800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:27328800-27331600	Strong transcription	Ovary	ovary
26	chr6:27329200-27335600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:27329400-27335400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:27329400-27337000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:27329400-27341800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:27329600-27335600	Weak transcription	Lung	lung
31	chr6:27329800-27331800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:27329800-27335000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:27329800-27335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:27329800-27335600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:27329800-27342000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr6:27330200-27335600	Weak transcription	Fetal Stomach	stomach
37	chr6:27330200-27341400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:27330600-27335600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:27330600-27341800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:27330600-27341800	Weak transcription	Brain Anterior Caudate	brain
41	chr6:27331200-27332200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:27331200-27333600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:27331200-27335600	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:27331200-27335600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:27331200-27335600	Weak transcription	Fetal Lung	lung
46	chr6:27331200-27335800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:27331200-27341600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr6:27331200-27341800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr6:27331400-27331600	ZNF genes & repeats	Left Ventricle	heart
50	chr6:27331400-27332200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links