Variant report

Variant	rs3825944
Chromosome Location	chr15:74667758-74667759
allele	C/T
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:33)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74665025..74668014-chr15:74668385..74670407,3	MCF-7	breast:
2	chr15:74666571..74668341-chr15:75112633..75114980,2	MCF-7	breast:
3	chr15:74665365..74667927-chr15:74780037..74785377,6	MCF-7	breast:
4	chr15:74667220..74669467-chr15:74724695..74727732,3	MCF-7	breast:
5	chr15:74667376..74668079-chr15:74927591..74928122,2	K562	blood:
6	chr15:74666941..74668250-chr15:74730746..74731506,5	MCF-7	breast:
7	chr15:74664841..74669022-chr15:74717731..74721779,3	K562	blood:
8	chr15:74666968..74670060-chr15:74726920..74730762,3	K562	blood:
9	chr15:74665568..74668523-chr15:74922376..74925547,4	MCF-7	breast:
10	chr15:74667675..74669712-chr15:74724905..74727427,2	MCF-7	breast:
11	chr15:74662886..74664620-chr15:74666174..74668404,2	MCF-7	breast:
12	chr15:74665982..74668403-chr15:74893258..74895614,2	MCF-7	breast:
13	chr15:74665122..74667877-chr15:74906569..74911881,5	MCF-7	breast:
14	chr15:74667729..74671338-chr15:74726630..74730433,3	K562	blood:
15	chr15:74667595..74674345-chr15:74676249..74682092,7	K562	blood:
16	chr15:74665832..74668344-chr15:74734420..74737401,2	K562	blood:
17	chr15:74665248..74670570-chr15:74911003..74915113,6	MCF-7	breast:
18	chr15:74667119..74668182-chr15:74730613..74731657,6	MCF-7	breast:
19	chr15:74666929..74668936-chr15:74752727..74754266,2	MCF-7	breast:
20	chr15:74666257..74668996-chr15:74908771..74912295,3	K562	blood:
21	chr15:74667095..74668014-chr15:74781923..74782836,3	MCF-7	breast:
22	chr15:74666408..74668530-chr15:74918193..74920965,2	MCF-7	breast:
23	chr15:74666244..74667848-chr15:74753089..74754898,2	MCF-7	breast:
24	chr15:74665453..74667821-chr15:74780445..74783665,3	MCF-7	breast:
25	chr15:74664932..74669170-chr15:74905600..74910371,8	K562	blood:
26	chr15:74665255..74670127-chr15:74905870..74910808,10	MCF-7	breast:
27	chr15:74667179..74667764-chr15:74913099..74914079,2	MCF-7	breast:
28	chr15:74667692..74668588-chr15:74730533..74731730,4	K562	blood:
29	chr15:74667276..74668170-chr15:74753089..74753827,2	MCF-7	breast:
30	chr15:74667641..74668257-chr15:74913258..74913984,2	K562	blood:
31	chr15:74666116..74667931-chr15:74831912..74834026,2	MCF-7	breast:
32	chr15:74667308..74668166-chr15:75092202..75092744,2	K562	blood:
33	chr15:74667265..74667860-chr15:75063172..75064014,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000138629	Chromatin interaction
ENSG00000138623	Chromatin interaction
ENSG00000179151	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000247240	Chromatin interaction
ENSG00000212279	Chromatin interaction
ENSG00000179361	Chromatin interaction
ENSG00000260103	Chromatin interaction
ENSG00000261775	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11072478	0.88[ASW][hapmap];0.82[YRI][hapmap]
rs12438594	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]
rs16968477	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16968478	0.81[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2073475	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28681535	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2930304	0.81[YRI][hapmap]
rs2959004	0.83[ASW][hapmap];0.82[YRI][hapmap]
rs3935523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4077581	0.80[LWK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs4077582	0.89[YRI][hapmap]
rs4077583	1.00[AFR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4077585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4555110	0.94[CEU][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4598865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60636222	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7167038	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7180275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7181947	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8031121	0.89[YRI][hapmap]
rs8031424	0.90[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3825944	LMAN1L	cis	parietal	SCAN
rs3825944	NRG4	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74665600-74667800	Flanking Active TSS	Hela-S3	cervix
2	chr15:74665800-74667800	Enhancers	Fetal Heart	heart
3	chr15:74666200-74667800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:74666600-74673200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:74666800-74667800	Enhancers	Primary hematopoietic stem cells	blood
6	chr15:74666800-74667800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr15:74666800-74667800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr15:74666800-74667800	Enhancers	Spleen	Spleen
9	chr15:74666800-74667800	Flanking Active TSS	HepG2	liver
10	chr15:74667000-74667800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:74667000-74667800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr15:74667000-74668000	Enhancers	Fetal Thymus	thymus
13	chr15:74667000-74671200	Weak transcription	Thymus	Thymus
14	chr15:74667000-74671400	Weak transcription	Lung	lung
15	chr15:74667200-74667800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr15:74667200-74667800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr15:74667200-74667800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:74667200-74667800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr15:74667200-74667800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:74667200-74667800	Enhancers	Colon Smooth Muscle	Colon
21	chr15:74667200-74667800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr15:74667200-74667800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:74667200-74667800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr15:74667200-74667800	Enhancers	K562	blood
25	chr15:74667200-74667800	Enhancers	NH-A	brain
26	chr15:74667200-74668000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr15:74667200-74668000	Enhancers	Primary B cells from peripheral blood	blood
28	chr15:74667200-74668000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr15:74667200-74668000	Enhancers	Dnd41	blood
30	chr15:74667200-74676400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:74667400-74667800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:74667400-74667800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:74667400-74667800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:74667400-74667800	Enhancers	Stomach Mucosa	stomach
35	chr15:74667400-74671200	Weak transcription	Esophagus	oesophagus
36	chr15:74667400-74673600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:74667400-74676800	Weak transcription	Colonic Mucosa	Colon
38	chr15:74667400-74691200	Enhancers	Placenta	Placenta
39	chr15:74667600-74667800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
40	chr15:74667600-74667800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
41	chr15:74667600-74667800	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr15:74667600-74667800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
43	chr15:74667600-74667800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
44	chr15:74667600-74667800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
45	chr15:74667600-74667800	Enhancers	Primary B cells from cord blood	blood
46	chr15:74667600-74667800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr15:74667600-74667800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:74667600-74667800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:74667600-74667800	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr15:74667600-74667800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links