Variant report

Variant	rs9646204
Chromosome Location	chr15:59070429-59070430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59040703..59045173-chr15:59068143..59071551,4	K562	blood:
2	chr15:59069188..59071465-chr15:59071661..59073187,2	MCF-7	breast:
3	chr15:59040418..59043088-chr15:59070016..59071551,2	K562	blood:
4	chr15:59063628..59066119-chr15:59070101..59071953,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137845	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11071396	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11852241	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11853043	0.85[MKK][hapmap]
rs12437552	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes]
rs12438114	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1365772	0.88[MKK][hapmap]
rs1427280	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs17236243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17301982	0.80[CEU][hapmap]
rs1869133	0.81[MKK][hapmap]
rs2114573	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2414606	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs2414607	0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28391588	0.80[MEX][hapmap]
rs28537903	0.81[EUR][1000 genomes]
rs28617688	0.84[EUR][1000 genomes]
rs34546804	0.90[EUR][1000 genomes]
rs3933541	0.85[AMR][1000 genomes]
rs394845	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs4774309	0.91[CHB][hapmap]
rs4774311	0.91[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes]
rs655348	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs681711	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs694335	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7164053	0.89[EUR][1000 genomes]
rs7164844	0.91[CEU][hapmap];0.83[CHB][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs7168275	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7170538	0.91[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs7171198	0.91[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes]
rs7173286	0.83[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7178970	0.88[EUR][1000 genomes]
rs7179724	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs7182060	0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs7183504	0.80[AMR][1000 genomes]
rs8023706	0.83[AMR][1000 genomes]
rs8027998	0.80[MEX][hapmap];0.80[AMR][1000 genomes]
rs8033478	0.89[EUR][1000 genomes]
rs8036097	0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs9744045	0.89[EUR][1000 genomes]
rs9788674	0.86[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	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
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59064600-59081000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:59064600-59085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:59064600-59102800	Weak transcription	Lung	lung
4	chr15:59064600-59102800	Weak transcription	Pancreas	Pancrea
5	chr15:59064600-59103200	Weak transcription	Esophagus	oesophagus
6	chr15:59064600-59145600	Weak transcription	Gastric	stomach
7	chr15:59064800-59095400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:59065200-59117800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:59065600-59082600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:59065800-59077800	Weak transcription	Psoas Muscle	Psoas
11	chr15:59065800-59082600	Weak transcription	Placenta	Placenta
12	chr15:59065800-59094600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:59065800-59095000	Weak transcription	Fetal Thymus	thymus
14	chr15:59065800-59102800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:59065800-59103200	Weak transcription	NH-A	brain
16	chr15:59065800-59142800	Weak transcription	Aorta	Aorta
17	chr15:59066000-59071000	Weak transcription	Fetal Stomach	stomach
18	chr15:59066000-59074800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:59066000-59085200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:59066000-59095000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:59066000-59102400	Weak transcription	HSMM	muscle
22	chr15:59066200-59071000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:59066200-59081600	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:59066200-59084200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:59066200-59095000	Weak transcription	Osteobl	bone
26	chr15:59066200-59095600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:59066400-59084200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:59066400-59085200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:59066400-59091000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:59066400-59095000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:59066400-59095000	Weak transcription	Fetal Intestine Large	intestine
32	chr15:59066600-59070800	Weak transcription	Left Ventricle	heart
33	chr15:59066600-59071200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr15:59066600-59078200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:59066600-59102400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr15:59066800-59077000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:59066800-59078600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:59067000-59070800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:59067000-59070800	Weak transcription	Fetal Intestine Small	intestine
40	chr15:59067000-59082600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:59067000-59083600	Weak transcription	HMEC	breast
42	chr15:59067000-59094600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:59067000-59094800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:59067000-59102400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:59067000-59102800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr15:59067000-59102800	Weak transcription	NHDF-Ad	bronchial
47	chr15:59067000-59157800	Weak transcription	Hela-S3	cervix
48	chr15:59067200-59071400	Weak transcription	Fetal Heart	heart
49	chr15:59067200-59072000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:59067200-59072600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links