Variant report

Variant	rs1054991
Chromosome Location	chr15:59149400-59149401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59146076..59151361-chr15:59223071..59227542,5	MCF-7	breast:
2	chr15:59144722..59148208-chr15:59148286..59151538,5	K562	blood:
3	chr15:59144722..59147196-chr15:59148286..59150161,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF111-3	chr15:59148026-59149425	NONHSAT044131

Variant related genes	Relation type
ENSG00000137776	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1053420	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10851640	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11071399	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632138	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11632231	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16940850	0.86[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4774312	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4775096	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4775097	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7164683	0.87[ASN][1000 genomes]
rs7178522	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7178955	0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1035640	chr15:59105360-59190930	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv904270	chr15:59140329-59238415	Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59067000-59157800	Weak transcription	Hela-S3	cervix
2	chr15:59077800-59153600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr15:59090200-59156600	Weak transcription	Small Intestine	intestine
4	chr15:59095200-59156800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:59103800-59157000	Weak transcription	Psoas Muscle	Psoas
6	chr15:59104000-59157000	Weak transcription	Esophagus	oesophagus
7	chr15:59104000-59157200	Weak transcription	NHLF	lung
8	chr15:59106000-59156800	Weak transcription	Lung	lung
9	chr15:59106200-59156800	Weak transcription	Ovary	ovary
10	chr15:59106200-59157000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:59106600-59157000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:59106800-59156400	Weak transcription	Fetal Kidney	kidney
13	chr15:59111800-59159600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:59119600-59149600	Weak transcription	Dnd41	blood
15	chr15:59120000-59169000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:59122000-59156400	Weak transcription	Fetal Heart	heart
17	chr15:59126000-59156600	Weak transcription	Right Ventricle	heart
18	chr15:59126200-59157000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:59126800-59151200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:59127200-59150400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr15:59127200-59156600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:59132800-59149600	Weak transcription	HUVEC	blood vessel
23	chr15:59136000-59151800	Weak transcription	GM12878-XiMat	blood
24	chr15:59137200-59156800	Weak transcription	Spleen	Spleen
25	chr15:59138200-59156400	Weak transcription	Brain Substantia Nigra	brain
26	chr15:59138200-59156800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:59138400-59155800	Weak transcription	Fetal Brain Male	brain
28	chr15:59140000-59155000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:59140600-59153600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:59140600-59154200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr15:59140600-59154200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr15:59140600-59154200	Weak transcription	Brain Angular Gyrus	brain
33	chr15:59140600-59156400	Weak transcription	Liver	Liver
34	chr15:59140600-59156800	Weak transcription	Primary B cells from cord blood	blood
35	chr15:59140600-59156800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:59140600-59156800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:59140800-59154200	Weak transcription	NHEK	skin
38	chr15:59140800-59156800	Weak transcription	Fetal Lung	lung
39	chr15:59141600-59154200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:59141800-59156800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr15:59142000-59149600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:59142600-59156800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:59142800-59157000	Weak transcription	Brain Germinal Matrix	brain
44	chr15:59143000-59154200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:59143200-59156400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr15:59144200-59156400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:59144400-59156400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:59144400-59156600	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:59144400-59156800	Weak transcription	Thymus	Thymus
50	chr15:59144400-59157000	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links