Variant report

Variant	rs1554108
Chromosome Location	chr2:9898684-9898685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9897830..9899713-chr2:9900837..9903744,2	K562	blood:
2	chr2:9897337..9900295-chr2:9937034..9939837,3	K562	blood:
3	chr2:9897831..9899412-chr2:9902196..9904626,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YWHAQ-1	chr2:9897625-9899428	XLOC_001982

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10171491	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10176382	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178017	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10180724	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10200779	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10200869	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10202283	0.84[ASN][1000 genomes]
rs1110317	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1123269	0.80[CEU][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11674642	0.86[JPT][hapmap]
rs11680429	0.90[JPT][hapmap]
rs12475853	0.90[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12476199	0.83[ASN][1000 genomes]
rs12476232	0.81[CEU][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12692393	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12692394	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12996417	0.83[ASN][1000 genomes]
rs13018695	0.85[ASN][1000 genomes]
rs13028425	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13030983	0.86[CHB][hapmap]
rs13395171	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13398163	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13398193	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13398304	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1554107	0.84[ASN][1000 genomes]
rs2357263	0.90[JPT][hapmap]
rs4668636	0.91[JPT][hapmap]
rs4668637	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4668644	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4669427	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4669428	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4669429	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4669445	0.95[JPT][hapmap]
rs4669451	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432033	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs6708081	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6713497	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6735280	0.90[JPT][hapmap]
rs6740013	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6742929	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743152	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6754662	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6756567	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6761286	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6761920	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7423455	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7423458	0.84[ASN][1000 genomes]
rs7602784	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs7605675	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs868442	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs884881	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv518227	chr2:9893454-9909114	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9894600-9899800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:9894800-9899600	Enhancers	Esophagus	oesophagus
3	chr2:9895200-9898800	Weak transcription	A549	lung
4	chr2:9895400-9904000	Weak transcription	Hela-S3	cervix
5	chr2:9895600-9900000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:9895600-9900200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:9895600-9900800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:9896200-9901400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:9896800-9899600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr2:9896800-9899800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr2:9897000-9899000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:9897000-9902200	Enhancers	K562	blood
13	chr2:9897200-9899000	Enhancers	HSMM	muscle
14	chr2:9897200-9899200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:9897400-9898800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:9897400-9899200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:9897600-9898800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:9897800-9899000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:9897800-9899000	Flanking Active TSS	Fetal Heart	heart
20	chr2:9898000-9899200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:9898200-9898800	Bivalent Enhancer	Fetal Stomach	stomach
22	chr2:9898200-9899000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:9898200-9899200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:9898200-9899400	Enhancers	Pancreas	Pancrea
25	chr2:9898200-9899600	Enhancers	Right Ventricle	heart
26	chr2:9898400-9898800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:9898400-9898800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:9898400-9898800	Enhancers	Fetal Intestine Small	intestine
29	chr2:9898400-9899000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
30	chr2:9898400-9899000	Enhancers	Left Ventricle	heart
31	chr2:9898400-9899200	Enhancers	HMEC	breast
32	chr2:9898400-9899600	Enhancers	Fetal Lung	lung
33	chr2:9898400-9899600	Enhancers	Right Atrium	heart
34	chr2:9898400-9899800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:9898400-9899800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:9898400-9900200	Weak transcription	Primary T cells from cord blood	blood
37	chr2:9898400-9900200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:9898400-9900400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:9898400-9900800	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr2:9898400-9901200	Enhancers	NHEK	skin
41	chr2:9898600-9898800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:9898600-9898800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:9898600-9898800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:9898600-9898800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:9898600-9898800	Enhancers	Brain Substantia Nigra	brain
46	chr2:9898600-9898800	Enhancers	Psoas Muscle	Psoas
47	chr2:9898600-9899000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
48	chr2:9898600-9899000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:9898600-9899000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
50	chr2:9898600-9899000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links