Variant report

Variant	rs1571897
Chromosome Location	chr9:97781919-97781920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97765071..97767480-chr9:97781588..97784169,2	K562	blood:
2	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
3	chr9:97781725..97783265-chr9:97854758..97856539,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIATL1-18	chr9:97781173-97782515	NONHSAT133342

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1004813	0.82[JPT][hapmap]
rs1020962	0.85[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1038092	0.85[CHB][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs10512252	0.82[JPT][hapmap]
rs10739991	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10761371	0.83[AMR][1000 genomes]
rs10993471	0.85[CHB][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs1113967	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12551506	1.00[JPT][hapmap]
rs12554043	0.87[GIH][hapmap];0.82[JPT][hapmap]
rs12555829	0.85[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12682668	0.82[JPT][hapmap]
rs12684139	0.82[JPT][hapmap]
rs12684154	0.82[JPT][hapmap]
rs12684461	0.82[JPT][hapmap]
rs12684470	0.82[JPT][hapmap]
rs12686500	0.82[JPT][hapmap]
rs1530331	0.87[GIH][hapmap];0.82[JPT][hapmap]
rs1542107	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs1564235	0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs1571896	0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16905557	0.82[JPT][hapmap]
rs16911801	0.82[JPT][hapmap]
rs16911802	0.82[JPT][hapmap]
rs16911817	0.82[JPT][hapmap]
rs16911821	0.82[JPT][hapmap]
rs16911826	0.82[JPT][hapmap]
rs1806996	0.82[JPT][hapmap]
rs1871220	0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs1888944	0.85[CHB][hapmap];0.86[MEX][hapmap]
rs1904201	1.00[JPT][hapmap]
rs2026399	0.87[GIH][hapmap];1.00[JPT][hapmap]
rs2061798	0.85[CHB][hapmap];0.88[AMR][1000 genomes]
rs2061799	0.82[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2061801	0.85[CHB][hapmap];0.90[AMR][1000 genomes]
rs2078379	0.82[JPT][hapmap]
rs2095069	0.87[GIH][hapmap];1.00[JPT][hapmap]
rs2119953	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs2306207	0.85[CHB][hapmap];1.00[MEX][hapmap]
rs2406898	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs2897523	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs3739748	0.85[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3824493	0.82[JPT][hapmap]
rs3847309	0.82[JPT][hapmap]
rs3847310	0.82[JPT][hapmap]
rs3886567	0.82[JPT][hapmap]
rs3886568	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs4743975	0.85[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743976	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743977	0.85[CHB][hapmap];0.90[AMR][1000 genomes]
rs4743978	0.81[AMR][1000 genomes]
rs4744389	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4744421	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744437	0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs4744440	0.85[CHB][hapmap]
rs6479576	0.82[JPT][hapmap]
rs6479589	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479596	0.87[ASN][1000 genomes]
rs6479597	0.87[ASN][1000 genomes]
rs66993340	0.90[ASN][1000 genomes]
rs67134693	0.90[AMR][1000 genomes]
rs7022739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7023719	0.86[MEX][hapmap]
rs7026714	0.82[JPT][hapmap]
rs7029570	0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7035166	0.87[GIH][hapmap];0.82[JPT][hapmap]
rs7038519	0.82[JPT][hapmap]
rs7045005	0.82[JPT][hapmap]
rs7046900	0.85[CHB][hapmap]
rs73540087	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7850680	0.82[JPT][hapmap]
rs7869736	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs7870679	0.82[JPT][hapmap]
rs894427	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs894428	0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97768000-97783800	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr9:97768000-97786200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:97768800-97785600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:97769000-97783800	Weak transcription	Fetal Brain Male	brain
5	chr9:97769000-97787600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:97769600-97784200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:97769600-97790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:97770800-97782000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:97770800-97782200	Weak transcription	Lung	lung
10	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
11	chr9:97772000-97782200	Weak transcription	Esophagus	oesophagus
12	chr9:97773000-97782200	Weak transcription	Spleen	Spleen
13	chr9:97773200-97793200	Weak transcription	Brain Germinal Matrix	brain
14	chr9:97776000-97784400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr9:97776000-97784600	Strong transcription	Placenta	Placenta
16	chr9:97776400-97785400	Strong transcription	Fetal Intestine Large	intestine
17	chr9:97777200-97782200	Weak transcription	Stomach Mucosa	stomach
18	chr9:97777400-97794200	Weak transcription	Thymus	Thymus
19	chr9:97778800-97786200	Genic enhancers	Osteobl	bone
20	chr9:97779000-97782800	Genic enhancers	HSMMtube	muscle
21	chr9:97779200-97782200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:97779200-97782200	Weak transcription	Fetal Intestine Small	intestine
23	chr9:97779200-97782400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:97779400-97782400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
25	chr9:97779400-97782800	Transcr. at gene 5' and 3'	A549	lung
26	chr9:97779400-97789200	Genic enhancers	Liver	Liver
27	chr9:97779800-97782800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:97780000-97782000	Active TSS	Aorta	Aorta
29	chr9:97780000-97782200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr9:97780200-97782000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:97780200-97782200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:97780200-97783600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr9:97780200-97785200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:97780200-97788000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr9:97780200-97788200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr9:97780600-97786600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr9:97780600-97790800	Weak transcription	Fetal Brain Female	brain
38	chr9:97780800-97782600	Genic enhancers	Adipose Nuclei	Adipose
39	chr9:97780800-97784400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:97780800-97786000	Genic enhancers	Left Ventricle	heart
41	chr9:97781000-97782000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr9:97781000-97782000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr9:97781000-97782800	Genic enhancers	Rectal Mucosa Donor 31	rectum
44	chr9:97781000-97784200	Strong transcription	Hela-S3	cervix
45	chr9:97781000-97786400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:97781200-97782000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:97781200-97782200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr9:97781200-97782200	Enhancers	Rectal Smooth Muscle	rectum
49	chr9:97781200-97782200	Strong transcription	HepG2	liver
50	chr9:97781200-97782400	Strong transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links