Variant report

Variant	rs388749
Chromosome Location	chr5:178028134-178028135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178027794..178030031-chr5:178033436..178035036,2	MCF-7	breast:
2	chr5:178026410..178028805-chr5:178033864..178036012,2	K562	blood:
3	chr5:178026187..178028267-chr5:178030915..178032717,2	K562	blood:
4	chr5:178024210..178026391-chr5:178026680..178028373,2	K562	blood:
5	chr5:178015408..178017355-chr5:178028126..178029814,2	MCF-7	breast:
6	chr5:178022246..178024591-chr5:178025333..178028233,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10035557	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10051137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10061455	0.87[ASN][1000 genomes]
rs10061883	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs10064009	0.88[ASN][1000 genomes]
rs10065419	0.82[ASN][1000 genomes]
rs10070794	0.88[ASN][1000 genomes]
rs10073925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479501	0.88[ASN][1000 genomes]
rs11742564	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11744815	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11748909	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11953546	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs12654185	0.87[ASN][1000 genomes]
rs12654187	0.87[ASN][1000 genomes]
rs12719855	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13161074	0.83[ASN][1000 genomes]
rs13360296	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1472457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967419	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335442	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs262021	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs262028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262036	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073633	0.88[ASN][1000 genomes]
rs4077796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4079109	0.88[ASN][1000 genomes]
rs4079111	0.88[ASN][1000 genomes]
rs4079112	0.93[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4301240	0.88[ASN][1000 genomes]
rs4413550	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs4418123	0.88[ASN][1000 genomes]
rs4437394	0.88[ASN][1000 genomes]
rs4521498	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4976798	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600942	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6866336	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6866952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6869889	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6871074	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6874126	0.82[ASN][1000 genomes]
rs6877022	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs721142	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs721143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73353860	0.86[ASN][1000 genomes]
rs73353883	0.87[ASN][1000 genomes]
rs752043	0.92[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7707891	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7715291	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7720708	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7736565	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs776153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178017800-178031400	Weak transcription	Pancreas	Pancrea
2	chr5:178017800-178033400	Weak transcription	Esophagus	oesophagus
3	chr5:178017800-178033400	Weak transcription	Gastric	stomach
4	chr5:178017800-178033400	Weak transcription	Right Atrium	heart
5	chr5:178018000-178028600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:178018200-178030000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:178018200-178032600	Weak transcription	Brain Angular Gyrus	brain
8	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
9	chr5:178018400-178029600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:178018600-178030000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:178019000-178029600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:178019000-178031400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:178019400-178036800	Weak transcription	Psoas Muscle	Psoas
14	chr5:178021600-178031200	Weak transcription	Ovary	ovary
15	chr5:178022000-178030600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:178022400-178030800	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:178022400-178038600	Weak transcription	Small Intestine	intestine
18	chr5:178022600-178031000	Weak transcription	Right Ventricle	heart
19	chr5:178022800-178031600	Weak transcription	Fetal Brain Male	brain
20	chr5:178023200-178028800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:178023200-178029000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:178023200-178030800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:178023200-178046000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:178023400-178028600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr5:178023400-178029400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:178023600-178028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:178023600-178028800	Weak transcription	Brain Substantia Nigra	brain
28	chr5:178023600-178029600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:178023600-178029600	Weak transcription	Brain Germinal Matrix	brain
30	chr5:178023600-178029800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:178023600-178030800	Weak transcription	Fetal Kidney	kidney
32	chr5:178023600-178031000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:178023800-178028600	Weak transcription	Fetal Brain Female	brain
34	chr5:178023800-178028800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:178024000-178050000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:178024200-178030000	Strong transcription	Osteobl	bone
37	chr5:178024200-178031000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr5:178024400-178031200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:178024400-178046000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:178024600-178028600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:178024600-178031000	Weak transcription	Colonic Mucosa	Colon
42	chr5:178024600-178035800	Strong transcription	Primary B cells from cord blood	blood
43	chr5:178024600-178037000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:178024800-178028800	Weak transcription	Thymus	Thymus
45	chr5:178025200-178030400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:178025200-178030800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:178025400-178028200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:178025400-178028400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:178025400-178028600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:178025400-178028800	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links