Variant report

Variant	rs17304995
Chromosome Location	chr3:53070755-53070756
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	chr3:53069872..53071542-chr3:53073094..53075949,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11130332	0.88[EUR][1000 genomes]
rs1134546	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[TSI][hapmap]
rs11707576	0.88[EUR][1000 genomes]
rs11708223	0.87[EUR][1000 genomes]
rs13082061	0.86[EUR][1000 genomes]
rs2246556	0.84[CEU][hapmap]
rs2255107	0.82[CEU][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs2276825	0.94[CEU][hapmap];0.85[TSI][hapmap]
rs2336669	1.00[CEU][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2336671	0.86[EUR][1000 genomes]
rs2564947	1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2581779	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2581780	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2581796	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2581797	0.88[EUR][1000 genomes]
rs2581801	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2581802	0.88[EUR][1000 genomes]
rs2581805	0.87[EUR][1000 genomes]
rs2581810	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2581815	1.00[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2581820	0.90[EUR][1000 genomes]
rs2581823	0.89[EUR][1000 genomes]
rs2710345	0.88[EUR][1000 genomes]
rs34230854	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35380116	0.85[EUR][1000 genomes]
rs3733047	0.82[CEU][hapmap]
rs4302374	0.94[CEU][hapmap]
rs4519686	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4687672	0.81[CEU][hapmap]
rs4687692	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687699	0.88[EUR][1000 genomes]
rs59989280	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6445538	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs6445539	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs6445547	0.93[CEU][hapmap]
rs6445550	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs6768844	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs6770957	0.90[EUR][1000 genomes]
rs6771610	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6789219	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792578	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs6803519	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs6805298	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71301803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71301807	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621939	0.88[EUR][1000 genomes]
rs7637082	0.90[EUR][1000 genomes]
rs7644973	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648514	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7652131	0.90[EUR][1000 genomes]
rs9311485	1.00[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs9682464	0.94[CEU][hapmap]
rs9812543	0.90[EUR][1000 genomes]
rs9813024	0.85[EUR][1000 genomes]
rs9831409	0.88[EUR][1000 genomes]
rs9842974	0.89[EUR][1000 genomes]
rs9844736	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[TSI][hapmap]
rs9846976	1.00[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs9847024	0.83[EUR][1000 genomes]
rs9865094	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9870898	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9876403	0.94[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][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	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1823728	chr3:53046712-53080351	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv822094	chr3:53059674-53096460	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs17304995	TMEM110	cis	cerebellum	SCAN
rs17304995	PPM1M	cis	Artery Tibial	GTEx
rs17304995	ITIH4	cis	cerebellum	SCAN
rs17304995	RBM6	cis	cerebellum	SCAN
rs17304995	GLT8D1	cis	brain	seeQTL
rs17304995	ITIH4-AS1	cis	Artery Aorta	GTEx
rs17304995	ITIH4	cis	lymphoblastoid	seeQTL
rs17304995	GNL3	cis	cerebellum	SCAN
rs17304995	TMEM110	cis	parietal	SCAN
rs17304995	NT5DC2	cis	parietal	SCAN
rs17304995	GLT8D1	trans	brain	seeQTL
rs17304995	ITIH4	cis	multi-tissue	Pritchard
rs17304995	GNL3	cis	parietal	SCAN
rs17304995	SEMA3G	cis	parietal	SCAN
rs17304995	SERBP1P3	cis	lung	GTEx
rs17304995	MUSTN1	cis	Artery Aorta	GTEx
rs17304995	ITIH4	cis	brain	seeQTL
rs17304995	AMT	cis	parietal	SCAN
rs17304995	WDR6	cis	cerebellum	SCAN
rs17304995	ITIH4	cis	parietal	SCAN
rs17304995	ITIH4-AS1	cis	lung	GTEx
rs17304995	ITIH4-AS1	cis	Artery Tibial	GTEx
rs17304995	ITIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
2	chr3:53048800-53077800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:53056600-53077800	Weak transcription	Fetal Stomach	stomach
4	chr3:53061800-53070800	Weak transcription	Left Ventricle	heart
5	chr3:53061800-53074400	Weak transcription	Osteobl	bone
6	chr3:53062200-53074400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:53062200-53076800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:53062200-53077000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:53062400-53071000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:53064000-53078400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:53065400-53073000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:53065400-53073000	Weak transcription	Esophagus	oesophagus
13	chr3:53065400-53074400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:53065400-53077600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:53065400-53078600	Weak transcription	Gastric	stomach
16	chr3:53065600-53072600	Weak transcription	NHEK	skin
17	chr3:53065600-53077000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:53065800-53073000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:53065800-53076200	Weak transcription	Primary B cells from cord blood	blood
20	chr3:53066200-53070800	Weak transcription	Right Atrium	heart
21	chr3:53066200-53076800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:53068000-53077600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:53068200-53072000	Enhancers	Primary T cells fromperipheralblood	blood
24	chr3:53068600-53071000	Enhancers	Fetal Intestine Small	intestine
25	chr3:53068600-53071200	Enhancers	Fetal Intestine Large	intestine
26	chr3:53068600-53075000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:53068800-53070800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:53068800-53071200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr3:53068800-53071600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr3:53068800-53071600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:53068800-53071600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:53068800-53071600	Enhancers	HepG2	liver
33	chr3:53068800-53077400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:53069000-53071000	Enhancers	A549	lung
35	chr3:53069000-53071400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr3:53069200-53077800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:53069200-53077800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:53069800-53071000	Enhancers	Small Intestine	intestine
39	chr3:53069800-53073000	Weak transcription	Pancreas	Pancrea
40	chr3:53069800-53077600	Weak transcription	Stomach Mucosa	stomach
41	chr3:53070000-53071400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:53070000-53071400	Enhancers	Dnd41	blood
43	chr3:53070200-53071000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:53070200-53072400	Weak transcription	Liver	Liver
45	chr3:53070200-53077800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:53070400-53071000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:53070400-53071000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr3:53070400-53071400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:53070400-53071400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr3:53070600-53071000	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links