Variant report

Variant	rs7544213
Chromosome Location	chr1:61821411-61821412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:61816681..61819448-chr1:61820713..61822267,2	MCF-7	breast:
2	chr1:61805404..61807718-chr1:61819195..61821796,2	K562	blood:

Variant related genes	Relation type
ENSG00000162599	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12735438	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12743816	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745353	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067774	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34094870	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34155705	1.00[EUR][1000 genomes]
rs35083921	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35688418	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66536513	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657128	0.87[AMR][1000 genomes]
rs6704173	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67885818	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71641729	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7545738	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
10	nsv1014023	chr1:61788310-61859074	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv534981	chr1:61788310-61859074	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61801200-61824600	Weak transcription	Gastric	stomach
2	chr1:61804400-61851400	Weak transcription	Small Intestine	intestine
3	chr1:61804400-61854600	Weak transcription	Placenta	Placenta
4	chr1:61804800-61822800	Weak transcription	Fetal Stomach	stomach
5	chr1:61805800-61848800	Weak transcription	Pancreas	Pancrea
6	chr1:61810000-61822600	Weak transcription	Fetal Kidney	kidney
7	chr1:61810200-61824600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:61810200-61827600	Weak transcription	Brain Germinal Matrix	brain
9	chr1:61810400-61824200	Weak transcription	Fetal Intestine Small	intestine
10	chr1:61810400-61828000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:61810600-61824400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:61810600-61828000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:61810600-61831600	Weak transcription	Stomach Mucosa	stomach
14	chr1:61810800-61824400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:61810800-61827800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:61811000-61822400	Weak transcription	Colonic Mucosa	Colon
17	chr1:61813800-61829800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:61814000-61848800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:61814200-61823600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:61814600-61841200	Weak transcription	Psoas Muscle	Psoas
21	chr1:61814600-61848800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:61814800-61827800	Weak transcription	Brain Substantia Nigra	brain
23	chr1:61818000-61822000	Strong transcription	Liver	Liver
24	chr1:61818000-61823400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:61818200-61822200	Weak transcription	HSMM	muscle
26	chr1:61818400-61822000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:61818400-61827400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:61818600-61837600	Weak transcription	Fetal Brain Male	brain
29	chr1:61818800-61822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:61818800-61822800	Weak transcription	Right Ventricle	heart
31	chr1:61818800-61824400	Weak transcription	HMEC	breast
32	chr1:61818800-61824800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:61818800-61835800	Weak transcription	Esophagus	oesophagus
34	chr1:61819000-61822000	Weak transcription	HUVEC	blood vessel
35	chr1:61819000-61822600	Weak transcription	Fetal Intestine Large	intestine
36	chr1:61819000-61822800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:61819000-61822800	Weak transcription	Left Ventricle	heart
38	chr1:61819000-61823000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:61819000-61824400	Weak transcription	A549	lung
40	chr1:61819000-61832800	Weak transcription	Brain Angular Gyrus	brain
41	chr1:61819000-61848800	Weak transcription	Lung	lung
42	chr1:61819200-61824400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:61819200-61824600	Weak transcription	Aorta	Aorta
44	chr1:61819200-61824600	Weak transcription	Hela-S3	cervix
45	chr1:61819200-61824800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:61819200-61832800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:61819400-61822600	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:61819400-61823200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:61819600-61822600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:61819600-61824600	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links