Variant report

Variant	rs2415265
Chromosome Location	chr14:35630388-35630389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:35628989-35630853	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr14:35630217-35630740	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr14:35629938-35630815	MCF10A-Er-Src	breast:	n/a	n/a
4	RELA	chr14:35630058-35630874	GM19099	blood:	n/a	chr14:35630667-35630676 chr14:35630667-35630676

No.	Distal block	Cell Line	Cell type
1	chr14:35629587..35631138-chr14:35874069..35875682,2	MCF-7	breast:
2	chr14:35630047..35632589-chr14:35700698..35702553,2	MCF-7	breast:
3	chr14:35628567..35630693-chr14:35872213..35874122,2	MCF-7	breast:
4	chr14:35628320..35630476-chr14:35639523..35641227,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259090	TF binding region
ENSG00000100906	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10130047	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136614	0.98[ASN][1000 genomes]
rs10137674	0.98[ASN][1000 genomes]
rs10137757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10143314	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10143690	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146445	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149918	1.00[ASN][1000 genomes]
rs1074269	0.81[JPT][hapmap]
rs12147110	0.81[JPT][hapmap]
rs12433712	0.84[CHB][hapmap]
rs12437158	0.84[CHB][hapmap]
rs12586302	0.84[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs12590905	0.84[CHB][hapmap]
rs12891473	0.84[CHB][hapmap]
rs2250579	0.84[CHB][hapmap]
rs2383692	0.84[CHB][hapmap]
rs2383694	0.84[CHB][hapmap]
rs2415263	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2415264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2415268	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2415274	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415275	0.84[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28378259	0.98[ASN][1000 genomes]
rs28452109	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28723612	0.99[ASN][1000 genomes]
rs28750252	0.99[ASN][1000 genomes]
rs4488360	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981270	0.99[ASN][1000 genomes]
rs4981278	0.81[JPT][hapmap]
rs4982250	0.81[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs58764649	0.98[ASN][1000 genomes]
rs6571696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6571700	0.85[ASN][1000 genomes]
rs6571702	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7141699	0.98[ASN][1000 genomes]
rs7142230	0.99[ASN][1000 genomes]
rs7144898	0.84[CHB][hapmap]
rs7147346	0.84[CHB][hapmap]
rs7157780	0.88[ASN][1000 genomes]
rs7159390	0.81[JPT][hapmap]
rs72664862	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664863	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7401469	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8004288	0.87[EUR][1000 genomes]
rs8009854	0.84[CHB][hapmap]
rs8012308	0.84[CHB][hapmap]
rs8015200	0.84[CHB][hapmap]
rs8015350	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8015470	0.98[ASN][1000 genomes]
rs8016860	1.00[ASN][1000 genomes]
rs9322942	0.84[CHB][hapmap]
rs9671922	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9919891	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	65 gene(s)	inside rSNPs	diseases
4	nsv564264	chr14:35482797-35732369	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1044515	chr14:35510785-35756317	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS 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	42 gene(s)	inside rSNPs	diseases
7	nsv1046992	chr14:35527239-35724227	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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	27 gene(s)	inside rSNPs	diseases
8	nsv1051274	chr14:35529529-35724227	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv1048823	chr14:35537281-35724892	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
10	nsv542032	chr14:35537281-35724892	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv1040540	chr14:35537481-35724753	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv542033	chr14:35537481-35724753	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1042625	chr14:35546094-35680358	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases
14	nsv1050123	chr14:35546114-35724892	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
15	nsv542034	chr14:35546114-35724892	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
16	nsv1050700	chr14:35548276-35639084	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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	21 gene(s)	inside rSNPs	diseases
17	nsv1043692	chr14:35548276-35720016	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
18	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
19	nsv1047992	chr14:35563220-35639084	Enhancers Weak transcription Strong transcription 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	21 gene(s)	inside rSNPs	diseases
20	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
21	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
22	nsv1053978	chr14:35571762-35639084	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
23	nsv1040300	chr14:35602956-35643888	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1046680	chr14:35608347-35665374	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2415265	PTRH1	trans	parietal	SCAN
rs2415265	SRP54	cis	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35593000-35638200	Weak transcription	Fetal Brain Male	brain
2	chr14:35593000-35660400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr14:35593200-35635400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr14:35603200-35663400	Weak transcription	Fetal Lung	lung
5	chr14:35604200-35651400	Weak transcription	Esophagus	oesophagus
6	chr14:35604400-35642000	Weak transcription	Lung	lung
7	chr14:35604400-35651800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr14:35604400-35660200	Weak transcription	Aorta	Aorta
9	chr14:35604600-35667400	Weak transcription	Spleen	Spleen
10	chr14:35607400-35642800	Weak transcription	Left Ventricle	heart
11	chr14:35607400-35662000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:35607600-35661200	Weak transcription	Fetal Muscle Leg	muscle
13	chr14:35612000-35659800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr14:35612200-35641800	Weak transcription	Fetal Stomach	stomach
15	chr14:35613600-35635800	Weak transcription	Brain Substantia Nigra	brain
16	chr14:35622000-35645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr14:35625000-35645200	Weak transcription	Gastric	stomach
18	chr14:35625400-35644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr14:35625600-35633400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr14:35625600-35633400	Weak transcription	Liver	Liver
21	chr14:35625600-35637800	Weak transcription	Brain Anterior Caudate	brain
22	chr14:35625600-35643000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr14:35625600-35644600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr14:35625600-35645200	Weak transcription	Brain Hippocampus Middle	brain
25	chr14:35625600-35650000	Weak transcription	Psoas Muscle	Psoas
26	chr14:35625600-35662200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr14:35625600-35662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr14:35625800-35643000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr14:35626000-35636600	Weak transcription	Colon Smooth Muscle	Colon
30	chr14:35626200-35650800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr14:35626400-35651200	Weak transcription	Ovary	ovary
32	chr14:35626400-35658000	Weak transcription	Fetal Brain Female	brain
33	chr14:35627000-35645400	Weak transcription	HSMMtube	muscle
34	chr14:35627400-35630400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr14:35627400-35638400	Weak transcription	Fetal Heart	heart
36	chr14:35627800-35630400	Strong transcription	Primary B cells from cord blood	blood
37	chr14:35628200-35630400	Enhancers	NH-A	brain
38	chr14:35628200-35630600	Enhancers	Hela-S3	cervix
39	chr14:35628400-35630600	Enhancers	HMEC	breast
40	chr14:35628400-35630600	Enhancers	NHDF-Ad	bronchial
41	chr14:35628600-35635800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr14:35628600-35670200	Weak transcription	Thymus	Thymus
43	chr14:35628600-35672000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr14:35628800-35630400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr14:35628800-35630600	Flanking Active TSS	A549	lung
46	chr14:35628800-35631200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr14:35628800-35636600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr14:35628800-35638600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr14:35628800-35638800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr14:35629000-35630800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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