Variant report

Variant	rs11078921
Chromosome Location	chr17:37908867-37908868
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37892523..37898235-chr17:37904182..37913977,22	MCF-7	breast:
2	chr17:37897334..37903790-chr17:37903988..37910787,11	K562	blood:
3	chr17:37823262..37824838-chr17:37908595..37910545,2	K562	blood:
4	chr17:37907336..37908918-chr17:37910848..37912777,2	MCF-7	breast:
5	chr17:37772682..37776519-chr17:37907348..37911982,7	MCF-7	breast:
6	chr17:37885072..37889612-chr17:37908286..37912584,6	MCF-7	breast:
7	chr17:37907935..37911541-chr17:37914774..37918367,3	K562	blood:
8	chr17:37886591..37888354-chr17:37907462..37910071,2	K562	blood:
9	chr17:37878383..37881370-chr17:37906332..37908876,2	K562	blood:
10	chr17:37905061..37908397-chr17:37908549..37911938,4	MCF-7	breast:
11	chr17:37908803..37910895-chr17:38473942..38476553,2	MCF-7	breast:
12	chr17:37908772..37911030-chr17:38098767..38100390,2	K562	blood:
13	chr17:37854770..37856284-chr17:37908500..37910494,2	MCF-7	breast:
14	chr17:37908791..37912830-chr17:37925750..37930091,5	K562	blood:
15	chr17:37905278..37906793-chr17:37908372..37910022,2	K562	blood:
16	chr17:37778262..37779269-chr17:37908489..37909454,3	K562	blood:
17	chr17:37895465..37903504-chr17:37904751..37910787,10	K562	blood:
18	chr17:37892158..37901988-chr17:37904094..37913282,26	MCF-7	breast:
19	chr17:37803422..37805216-chr17:37908761..37911561,2	K562	blood:
20	chr17:37823299..37826049-chr17:37908764..37910653,3	K562	blood:
21	chr17:37828636..37830492-chr17:37908075..37910484,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141736	Chromatin interaction
ENSG00000141738	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000141744	Chromatin interaction
ENSG00000214546	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10445308	0.80[JPT][hapmap]
rs11557466	0.81[CHB][hapmap]
rs12150079	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs12946510	0.80[JPT][hapmap]
rs3809717	0.88[AFR][1000 genomes]
rs62066988	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs907091	0.80[JPT][hapmap]
rs907092	0.80[JPT][hapmap]
rs9303277	0.80[JPT][hapmap]
rs9909593	0.80[JPT][hapmap]

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	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1056234	chr17:37862605-37909988	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv908219	chr17:37880265-37917633	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11078921	IKZF3	cis	multi-tissue	Pritchard
rs11078921	AATF	cis	cerebellum	SCAN
rs11078921	TADA2A	cis	parietal	SCAN
rs11078921	DHRS11	cis	parietal	SCAN
rs11078921	ORMDL3	cis	lymphoblastoid	seeQTL
rs11078921	C17orf66	cis	parietal	SCAN
rs11078921	MED24	cis	parietal	SCAN
rs11078921	STAC2	cis	parietal	SCAN
rs11078921	CCL18	cis	cerebellum	SCAN
rs11078921	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs11078921	PCGF2	cis	cerebellum	SCAN
rs11078921	PIGW	cis	parietal	SCAN
rs11078921	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs11078921	ORMDL3	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37897200-37909400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:37897800-37910000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:37902200-37910000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:37903200-37909400	Weak transcription	HUVEC	blood vessel
5	chr17:37903400-37909400	Weak transcription	Colonic Mucosa	Colon
6	chr17:37903400-37910000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:37904000-37910000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:37906000-37909000	Enhancers	Fetal Heart	heart
9	chr17:37906200-37910000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:37906400-37909000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr17:37906400-37909800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr17:37906400-37909800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:37906600-37909200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr17:37906600-37909400	Weak transcription	Colon Smooth Muscle	Colon
15	chr17:37906600-37909400	Weak transcription	Fetal Intestine Small	intestine
16	chr17:37906600-37909800	Weak transcription	NH-A	brain
17	chr17:37906800-37909200	Weak transcription	Spleen	Spleen
18	chr17:37906800-37909400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr17:37906800-37909800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:37907000-37909400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:37907000-37909400	Weak transcription	Adipose Nuclei	Adipose
22	chr17:37907000-37909400	Weak transcription	Liver	Liver
23	chr17:37907000-37909400	Weak transcription	Fetal Intestine Large	intestine
24	chr17:37907000-37909400	Weak transcription	Gastric	stomach
25	chr17:37907000-37909400	Weak transcription	Left Ventricle	heart
26	chr17:37907000-37909400	Weak transcription	Right Atrium	heart
27	chr17:37907000-37909800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:37907200-37909400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr17:37907200-37909600	Weak transcription	Stomach Mucosa	stomach
30	chr17:37907200-37910000	Weak transcription	Lung	lung
31	chr17:37907400-37909000	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr17:37907400-37909400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr17:37907400-37909400	Weak transcription	Placenta	Placenta
34	chr17:37907400-37909400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr17:37907400-37909800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:37907400-37910000	Weak transcription	HMEC	breast
37	chr17:37907600-37909400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr17:37907600-37910000	Weak transcription	HSMMtube	muscle
39	chr17:37907800-37909400	Weak transcription	Pancreas	Pancrea
40	chr17:37907800-37910000	Enhancers	Primary B cells from cord blood	blood
41	chr17:37908000-37909000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr17:37908000-37909400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr17:37908000-37909600	Enhancers	Primary T cells fromperipheralblood	blood
44	chr17:37908000-37909600	Enhancers	Fetal Thymus	thymus
45	chr17:37908200-37909200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr17:37908200-37909400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr17:37908200-37909400	Weak transcription	Esophagus	oesophagus
48	chr17:37908200-37909400	Weak transcription	Right Ventricle	heart
49	chr17:37908200-37909600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr17:37908200-37909800	Enhancers	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links