Variant report

Variant	rs1541409
Chromosome Location	chr7:98027580-98027581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:97948846..97953573-chr7:98026962..98031463,6	MCF-7	breast:
2	chr7:97998858..98000704-chr7:98027178..98028821,2	MCF-7	breast:
3	chr7:97987419..97989875-chr7:98026560..98028581,2	K562	blood:
4	chr7:98023705..98027880-chr7:98028270..98031310,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006453	Chromatin interaction
ENSG00000272950	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006169	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10953254	0.85[AMR][1000 genomes]
rs11768599	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11769950	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11772432	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12533982	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12536125	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs12539761	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1874344	0.86[JPT][hapmap]
rs1985593	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2107718	0.81[EUR][1000 genomes]
rs2240348	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2270597	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3735258	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3801258	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3944111	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4236537	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4729432	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55648546	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55946416	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56997921	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59120980	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62478160	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62478201	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62478228	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62478235	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62479858	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs903592	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs9640655	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9641236	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9641237	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9649213	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS 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	23 gene(s)	inside rSNPs	diseases
6	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv888766	chr7:97975542-98123880	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
9	nsv5860	chr7:97995939-98028100	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv1795864	chr7:98013507-98040788	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv607919	chr7:98021211-98124854	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541409	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97990400-98028000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:97992000-98029400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:97995800-98028200	Weak transcription	Esophagus	oesophagus
4	chr7:98002600-98027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:98007400-98028000	Weak transcription	Fetal Stomach	stomach
6	chr7:98016800-98027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:98017600-98027800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:98017800-98028000	Weak transcription	Pancreas	Pancrea
9	chr7:98018000-98027600	Weak transcription	NHEK	skin
10	chr7:98018000-98028000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:98018600-98028000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:98018800-98028000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:98022000-98028000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:98022000-98029200	Weak transcription	Placenta	Placenta
15	chr7:98022200-98027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:98023800-98027800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:98024000-98027800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr7:98024200-98027600	Weak transcription	Hela-S3	cervix
19	chr7:98024200-98028200	Weak transcription	NH-A	brain
20	chr7:98024400-98028000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:98024400-98028000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:98024400-98028000	Weak transcription	Fetal Muscle Leg	muscle
23	chr7:98024800-98027600	Weak transcription	K562	blood
24	chr7:98025000-98027800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr7:98025000-98029000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:98025200-98028400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:98025400-98027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:98025400-98028000	Weak transcription	Colonic Mucosa	Colon
29	chr7:98025800-98027600	Genic enhancers	A549	lung
30	chr7:98026000-98027800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:98026000-98027800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:98026400-98027800	Weak transcription	Stomach Mucosa	stomach
33	chr7:98026600-98028000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:98027000-98027600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:98027000-98028000	Enhancers	NHDF-Ad	bronchial
36	chr7:98027000-98028200	Active TSS	GM12878-XiMat	blood
37	chr7:98027200-98027600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:98027200-98027800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr7:98027200-98027800	Weak transcription	Liver	Liver
40	chr7:98027200-98028000	Enhancers	HepG2	liver
41	chr7:98027200-98029000	Weak transcription	Right Atrium	heart
42	chr7:98027400-98027600	Enhancers	Duodenum Mucosa	Duodenum
43	chr7:98027400-98027800	Enhancers	Fetal Intestine Large	intestine
44	chr7:98027400-98027800	Enhancers	Fetal Intestine Small	intestine
45	chr7:98027400-98027800	Active TSS	HMEC	breast

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