Variant report

Variant	rs12438594
Chromosome Location	chr15:74667192-74667193
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74665429..74667664-chr15:74747982..74750255,2	MCF-7	breast:
2	chr15:74665025..74668014-chr15:74668385..74670407,3	MCF-7	breast:
3	chr15:74665902..74667600-chr15:74730654..74731665,8	K562	blood:
4	chr15:74665092..74667430-chr15:74726842..74729796,2	K562	blood:
5	chr15:74664672..74667592-chr15:74837544..74840546,3	MCF-7	breast:
6	chr15:74666571..74668341-chr15:75112633..75114980,2	MCF-7	breast:
7	chr15:74665365..74667927-chr15:74780037..74785377,6	MCF-7	breast:
8	chr15:74666941..74668250-chr15:74730746..74731506,5	MCF-7	breast:
9	chr15:74664841..74669022-chr15:74717731..74721779,3	K562	blood:
10	chr15:74666968..74670060-chr15:74726920..74730762,3	K562	blood:
11	chr15:74665425..74667643-chr15:74752949..74754890,2	K562	blood:
12	chr15:74665568..74668523-chr15:74922376..74925547,4	MCF-7	breast:
13	chr15:74666064..74667583-chr15:74922840..74924657,2	MCF-7	breast:
14	chr15:74662886..74664620-chr15:74666174..74668404,2	MCF-7	breast:
15	chr15:74665982..74668403-chr15:74893258..74895614,2	MCF-7	breast:
16	chr15:74665122..74667877-chr15:74906569..74911881,5	MCF-7	breast:
17	chr15:74665832..74668344-chr15:74734420..74737401,2	K562	blood:
18	chr15:74665248..74670570-chr15:74911003..74915113,6	MCF-7	breast:
19	chr15:74667119..74668182-chr15:74730613..74731657,6	MCF-7	breast:
20	chr15:74666929..74668936-chr15:74752727..74754266,2	MCF-7	breast:
21	chr15:74666257..74668996-chr15:74908771..74912295,3	K562	blood:
22	chr15:74667095..74668014-chr15:74781923..74782836,3	MCF-7	breast:
23	chr15:74666408..74668530-chr15:74918193..74920965,2	MCF-7	breast:
24	chr15:74666244..74667848-chr15:74753089..74754898,2	MCF-7	breast:
25	chr15:74665453..74667821-chr15:74780445..74783665,3	MCF-7	breast:
26	chr15:74664932..74669170-chr15:74905600..74910371,8	K562	blood:
27	chr15:74665255..74670127-chr15:74905870..74910808,10	MCF-7	breast:
28	chr15:74667179..74667764-chr15:74913099..74914079,2	MCF-7	breast:
29	chr15:74665619..74667467-chr17:66287023..66289875,2	MCF-7	breast:
30	chr15:74666116..74667931-chr15:74831912..74834026,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000138629	Chromatin interaction
ENSG00000212279	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000108932	Chromatin interaction
ENSG00000261775	Chromatin interaction
ENSG00000141337	Chromatin interaction
ENSG00000179361	Chromatin interaction
ENSG00000260103	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000247240	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11072478	0.82[YRI][hapmap]
rs16968477	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16968478	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2073475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28681535	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2930304	0.83[YRI][hapmap]
rs2959004	0.82[YRI][hapmap]
rs3825944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3935523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077581	0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs4077582	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs4077583	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4077585	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4555110	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4598865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60636222	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7167038	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7180275	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181947	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8031121	0.90[YRI][hapmap]
rs8031424	0.91[YRI][hapmap]
rs900802	0.82[YRI][hapmap]

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	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
3	nsv904351	chr15:74638965-74697084	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904352	chr15:74638965-74715205	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74665600-74667800	Flanking Active TSS	Hela-S3	cervix
2	chr15:74665800-74667200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
3	chr15:74665800-74667600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:74665800-74667600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:74665800-74667600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:74665800-74667800	Enhancers	Fetal Heart	heart
7	chr15:74666000-74667200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr15:74666000-74667200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:74666000-74667200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr15:74666000-74667200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr15:74666000-74667200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:74666000-74667200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:74666000-74667200	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr15:74666000-74667200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr15:74666000-74667200	Flanking Active TSS	Dnd41	blood
16	chr15:74666000-74667200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
17	chr15:74666000-74667200	Flanking Active TSS	NH-A	brain
18	chr15:74666000-74667400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:74666000-74667600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr15:74666000-74667600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr15:74666000-74667600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:74666000-74667600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr15:74666000-74667600	Flanking Active TSS	HMEC	breast
24	chr15:74666200-74667200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr15:74666200-74667200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr15:74666200-74667200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr15:74666200-74667200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:74666200-74667200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr15:74666200-74667400	Flanking Active TSS	Colonic Mucosa	Colon
30	chr15:74666200-74667600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr15:74666200-74667600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:74666200-74667600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr15:74666200-74667600	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr15:74666200-74667600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr15:74666200-74667600	Flanking Active TSS	GM12878-XiMat	blood
36	chr15:74666200-74667800	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr15:74666400-74667200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr15:74666400-74667600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:74666600-74667200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr15:74666600-74673200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:74666800-74667200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:74666800-74667200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:74666800-74667200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:74666800-74667200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:74666800-74667200	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr15:74666800-74667200	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr15:74666800-74667200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:74666800-74667200	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr15:74666800-74667200	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr15:74666800-74667200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links