Variant report

Variant	rs6555607
Chromosome Location	chr5:9554076-9554077
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	chr5:9552447..9554138-chr5:9558237..9561822,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12055364	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12186736	0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs16883128	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17263889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17329702	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271220	0.87[ASN][1000 genomes]
rs3798098	0.92[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6872486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72731105	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714356	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs907652	0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1023329	chr5:9543307-9731720	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	nsv881586	chr5:9549386-9578794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9547000-9554200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:9548200-9554200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:9548200-9556200	Weak transcription	Right Ventricle	heart
4	chr5:9548200-9558400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:9548200-9558400	Weak transcription	Liver	Liver
6	chr5:9548400-9558400	Weak transcription	Fetal Heart	heart
7	chr5:9548600-9558400	Weak transcription	Brain Hippocampus Middle	brain
8	chr5:9550200-9554400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:9550200-9558400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:9550200-9563000	Weak transcription	Brain Substantia Nigra	brain
11	chr5:9550400-9554800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:9550600-9558400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:9550800-9557400	Weak transcription	NHEK	skin
14	chr5:9551200-9554200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:9551200-9557400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:9551200-9558200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:9551200-9562200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:9551600-9561800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:9552000-9559200	Weak transcription	Colonic Mucosa	Colon
20	chr5:9552200-9554600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:9552200-9557200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:9552200-9557200	Weak transcription	NHLF	lung
23	chr5:9552200-9557400	Weak transcription	HMEC	breast
24	chr5:9552200-9557800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:9552200-9564600	Weak transcription	Aorta	Aorta
26	chr5:9552400-9557400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:9552600-9554200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:9552600-9555000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr5:9552800-9554600	Enhancers	Stomach Mucosa	stomach
30	chr5:9552800-9557200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:9552800-9557200	Weak transcription	Osteobl	bone
32	chr5:9552800-9557400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:9552800-9557400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:9552800-9557800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:9552800-9558000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:9552800-9562400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:9552800-9578400	Weak transcription	Ovary	ovary
38	chr5:9553000-9554600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:9553000-9554600	Enhancers	Fetal Intestine Large	intestine
40	chr5:9553000-9554600	Enhancers	Fetal Intestine Small	intestine
41	chr5:9553000-9554800	Enhancers	Duodenum Mucosa	Duodenum
42	chr5:9553000-9556800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:9553000-9557400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:9553000-9560000	Weak transcription	Fetal Lung	lung
45	chr5:9553000-9562200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:9553200-9557000	Weak transcription	NH-A	brain
47	chr5:9553200-9557200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:9553200-9557600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:9553600-9554600	Enhancers	Adipose Nuclei	Adipose
50	chr5:9553600-9555200	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links