Variant report

Variant	rs55664143
Chromosome Location	chr4:76656006-76656007
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76642183..76644584-chr4:76655445..76657261,2	MCF-7	breast:
2	chr4:76648622..76651912-chr4:76653743..76658788,6	MCF-7	breast:
3	chr4:76655795..76658592-chr4:76658878..76661383,2	K562	blood:

Variant related genes	Relation type
ENSG00000138757	Chromatin interaction
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10016782	0.88[AMR][1000 genomes]
rs10028291	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10031352	0.85[AFR][1000 genomes]
rs10031616	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10033315	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10212995	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11097112	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11097113	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11097122	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11727895	0.83[AFR][1000 genomes]
rs11728073	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11730896	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11938067	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11943497	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12505149	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12508992	0.83[AFR][1000 genomes]
rs13102733	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13110602	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13133144	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13133472	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13145290	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13147276	0.88[AMR][1000 genomes]
rs17000786	0.82[AFR][1000 genomes]
rs2271472	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2869175	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs324713	0.81[AFR][1000 genomes]
rs324722	0.80[AFR][1000 genomes]
rs324723	0.82[AFR][1000 genomes]
rs3796481	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4446339	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4859405	0.83[AMR][1000 genomes]
rs4859406	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4859408	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4859409	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4859549	0.81[AMR][1000 genomes]
rs4859552	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859554	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4859555	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6531901	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6843016	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6845147	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6846575	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6847333	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7655464	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7657198	0.80[AFR][1000 genomes]
rs7661037	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7665517	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7693127	0.83[AFR][1000 genomes]
rs905954	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs987561	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS 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 miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76658600	Weak transcription	Brain Substantia Nigra	brain
2	chr4:76650800-76673400	Weak transcription	Lung	lung
3	chr4:76650800-76675600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:76650800-76675800	Weak transcription	Esophagus	oesophagus
5	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:76651200-76657200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:76651200-76660800	Weak transcription	Thymus	Thymus
8	chr4:76651200-76661400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:76651200-76663600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:76651400-76667000	Weak transcription	Gastric	stomach
11	chr4:76651800-76667000	Weak transcription	Primary B cells from cord blood	blood
12	chr4:76652000-76657200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:76652000-76660600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:76652000-76673400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:76652000-76675200	Weak transcription	Fetal Thymus	thymus
16	chr4:76652000-76675400	Weak transcription	Placenta	Placenta
17	chr4:76652000-76675600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:76652000-76675600	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:76652000-76675600	Weak transcription	Spleen	Spleen
20	chr4:76652000-76696400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:76652200-76657200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:76652200-76659200	Weak transcription	Fetal Stomach	stomach
23	chr4:76652200-76660400	Weak transcription	Right Ventricle	heart
24	chr4:76652200-76664400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr4:76652200-76670800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:76652200-76675600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:76652400-76660200	Weak transcription	HSMM	muscle
28	chr4:76652400-76660800	Weak transcription	Stomach Mucosa	stomach
29	chr4:76652400-76662000	Weak transcription	Brain Angular Gyrus	brain
30	chr4:76652400-76665600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr4:76652400-76675200	Weak transcription	Fetal Kidney	kidney
32	chr4:76652400-76675600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:76652400-76675800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:76652400-76675800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr4:76652400-76725000	Weak transcription	Hela-S3	cervix
36	chr4:76652600-76663200	Weak transcription	Fetal Intestine Small	intestine
37	chr4:76652600-76670000	Weak transcription	K562	blood
38	chr4:76652600-76675400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:76652600-76675600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:76652800-76670000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr4:76652800-76675200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:76652800-76675600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:76652800-76675600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:76653000-76663600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:76653000-76669400	Weak transcription	HUVEC	blood vessel
46	chr4:76653200-76657400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:76653200-76658600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:76653200-76665600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:76653200-76665600	Weak transcription	A549	lung
50	chr4:76653200-76670000	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links