Variant report

Variant	rs7543419
Chromosome Location	chr1:227448484-227448485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227447057..227450743-chr1:227504946..227508409,3	MCF-7	breast:
2	chr1:227446907..227449535-chr1:227450206..227452004,2	K562	blood:
3	chr1:227447102..227448619-chr1:227452855..227454756,2	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction
ENSG00000236636	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10916112	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916113	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916116	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916125	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11576239	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11584325	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11585910	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12117207	0.83[CEU][hapmap]
rs12119153	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12123597	0.85[AMR][1000 genomes]
rs12128174	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12131061	0.92[AMR][1000 genomes]
rs12131459	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12131913	0.86[CEU][hapmap]
rs12131933	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12133230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12133633	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12138092	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12138364	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138383	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12138664	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12144205	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12744825	0.89[CEU][hapmap]
rs12746316	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12751015	0.87[CEU][hapmap]
rs12754677	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12755770	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1320495	0.87[CEU][hapmap]
rs1513607	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1513613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17545704	0.85[CEU][hapmap]
rs17613235	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2063661	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28648445	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34113967	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34702208	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34897490	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35160496	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35952573	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4308948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs61834323	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61834324	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61834326	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61834590	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61834625	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61834626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6660168	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6675572	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6678714	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6697583	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7512871	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs7518813	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7523759	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7526822	0.87[CEU][hapmap]
rs7539662	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7548118	1.00[AMR][1000 genomes];0.84[EUR][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3489592	chr1:227443729-227450377	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3452712	chr1:227443929-227450027	Enhancers Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3489589	chr1:227444279-227450327	Enhancers Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3452714	chr1:227444845-227449424	Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3452715	chr1:227444845-227449424	Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3452713	chr1:227444880-227449414	Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3489588	chr1:227444891-227449425	Enhancers Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv3489590	chr1:227444908-227449372	Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv3489593	chr1:227444909-227449395	Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv3489591	chr1:227444941-227449364	Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	esv3489594	chr1:227444941-227449372	Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	esv1804194	chr1:227445002-227448484	Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	esv1809608	chr1:227445002-227448484	Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv1809956	chr1:227445002-227448484	Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv1812335	chr1:227445002-227448484	Flanking Active TSS Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	esv1814324	chr1:227445002-227448484	Enhancers Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	esv10821	chr1:227445029-227449266	Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv522490	chr1:227446008-227450144	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv947163	chr1:227448485-227455052	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227414200-227453800	Weak transcription	HSMM	muscle
3	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
5	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
6	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
9	chr1:227433200-227452800	Weak transcription	Ovary	ovary
10	chr1:227434000-227453400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:227434200-227455400	Weak transcription	Left Ventricle	heart
12	chr1:227434200-227455400	Weak transcription	Right Ventricle	heart
13	chr1:227434200-227455800	Weak transcription	Adipose Nuclei	Adipose
14	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:227435600-227453600	Weak transcription	Fetal Intestine Small	intestine
18	chr1:227438800-227449400	Weak transcription	Right Atrium	heart
19	chr1:227440000-227456600	Weak transcription	HepG2	liver
20	chr1:227440200-227456800	Weak transcription	HUVEC	blood vessel
21	chr1:227441200-227450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:227441800-227449600	Weak transcription	A549	lung
23	chr1:227441800-227452000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:227442400-227449600	Weak transcription	Brain Angular Gyrus	brain
25	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:227445800-227458400	Weak transcription	NHEK	skin
27	chr1:227446000-227448600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:227446600-227448600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr1:227447000-227456800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:227447200-227452600	Weak transcription	Brain Substantia Nigra	brain
31	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:227447400-227452800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:227447400-227455000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:227448000-227448800	Flanking Active TSS	K562	blood
35	chr1:227448400-227448600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr1:227448400-227452400	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:227448400-227453600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:227448400-227456400	Weak transcription	Psoas Muscle	Psoas

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