Variant report

Variant	rs7546304
Chromosome Location	chr1:151114484-151114485
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:151114202-151114609	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr1:151114242-151114617	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151112727..151117017-chr1:151118116..151120270,3	K562	blood:
2	chr1:151032560..151034898-chr1:151112557..151115397,2	MCF-7	breast:
3	chr1:151110135..151112456-chr1:151113233..151115304,2	K562	blood:
4	chr1:151112857..151115063-chr1:151118194..151121631,4	MCF-7	breast:
5	chr1:151029687..151031858-chr1:151114009..151116505,2	K562	blood:
6	chr1:151020578..151022792-chr1:151112111..151115078,2	MCF-7	breast:
7	chr1:151112451..151114594-chr1:151115769..151118069,3	K562	blood:
8	chr1:151109028..151112291-chr1:151113939..151118222,5	K562	blood:
9	chr1:151040013..151045011-chr1:151111761..151118476,6	MCF-7	breast:

No data

Variant related genes	Relation type
SEMA6C	TF binding region
ENSG00000143458	Chromatin interaction
ENSG00000143443	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10788800	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888405	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12569193	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4357530	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4360524	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4512652	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61819219	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656450	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6674970	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6676190	0.86[EUR][1000 genomes];0.89[ASN][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7546304	BNIPL	cis	lung	GTEx
rs7546304	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151079800-151114800	Weak transcription	HSMM	muscle
2	chr1:151104000-151114800	Weak transcription	Psoas Muscle	Psoas
3	chr1:151104400-151116600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:151104400-151117000	Weak transcription	Fetal Kidney	kidney
5	chr1:151104400-151118000	Weak transcription	Aorta	Aorta
6	chr1:151104600-151117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:151104600-151118200	Weak transcription	Primary T cells from cord blood	blood
8	chr1:151104800-151115600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:151105000-151114800	Strong transcription	Fetal Brain Female	brain
10	chr1:151105000-151114800	Weak transcription	Right Atrium	heart
11	chr1:151105000-151115400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:151105000-151115600	Weak transcription	Fetal Thymus	thymus
13	chr1:151105200-151115200	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:151105200-151115400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:151105200-151117000	Weak transcription	Placenta	Placenta
16	chr1:151105400-151117000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:151105600-151114800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:151105600-151115800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:151105600-151118000	Weak transcription	Gastric	stomach
20	chr1:151105800-151115600	Weak transcription	Thymus	Thymus
21	chr1:151105800-151117200	Weak transcription	Spleen	Spleen
22	chr1:151106000-151114800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:151106000-151115000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:151106200-151116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:151106600-151115400	Strong transcription	Fetal Stomach	stomach
26	chr1:151106600-151116000	Strong transcription	Fetal Intestine Small	intestine
27	chr1:151107000-151116600	Weak transcription	HUVEC	blood vessel
28	chr1:151107000-151117600	Weak transcription	Colonic Mucosa	Colon
29	chr1:151107400-151114800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:151107400-151115000	Strong transcription	Brain Germinal Matrix	brain
31	chr1:151107800-151115800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:151108400-151115400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:151108400-151117200	Weak transcription	Brain Substantia Nigra	brain
34	chr1:151108600-151114800	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:151108600-151117800	Weak transcription	Esophagus	oesophagus
36	chr1:151108800-151115600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:151109400-151115200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:151109400-151115400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:151109400-151116000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:151109600-151115400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:151109600-151115600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:151109600-151116200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:151109600-151117600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:151110200-151115600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:151110200-151117600	Weak transcription	Pancreas	Pancrea
46	chr1:151110400-151114800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:151110600-151114800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:151110600-151114800	Weak transcription	HSMMtube	muscle
49	chr1:151110800-151114800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:151110800-151116200	Weak transcription	Brain Hippocampus Middle	brain

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