Variant report

Variant	rs6741891
Chromosome Location	chr2:54315666-54315667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54314163..54315744-chr2:54319070..54321460,2	MCF-7	breast:
2	chr2:54310601..54313895-chr2:54315141..54317483,3	MCF-7	breast:
3	chr2:54314046..54316494-chr2:54341212..54344177,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10203576	0.91[ASN][1000 genomes]
rs10207537	0.84[ASN][1000 genomes]
rs1058320	0.99[ASN][1000 genomes]
rs1075265	0.89[ASN][1000 genomes]
rs10865277	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10865278	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10865279	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11125520	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11125524	0.83[ASN][1000 genomes]
rs11695734	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11887549	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11888384	0.89[ASN][1000 genomes]
rs11896781	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12616638	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1363062	0.93[ASN][1000 genomes]
rs1421622	0.93[ASN][1000 genomes]
rs1559037	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1833497	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1833498	0.98[ASN][1000 genomes]
rs1862121	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1862122	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1877906	0.88[ASN][1000 genomes]
rs2018747	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042143	0.90[ASN][1000 genomes]
rs2048749	0.90[ASN][1000 genomes]
rs2112124	0.88[ASN][1000 genomes]
rs2287642	0.93[ASN][1000 genomes]
rs2357954	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34769118	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41385746	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4671178	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671190	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671860	0.85[ASN][1000 genomes]
rs4671872	0.88[ASN][1000 genomes]
rs56001939	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62137965	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137973	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6545384	0.98[ASN][1000 genomes]
rs6545388	0.81[ASN][1000 genomes]
rs7558126	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7560947	0.99[ASN][1000 genomes]
rs7562055	0.90[ASN][1000 genomes]
rs7569743	0.88[ASN][1000 genomes]
rs7573491	0.89[ASN][1000 genomes]
rs7590846	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7591194	0.99[ASN][1000 genomes]
rs7600141	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7604357	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7607066	0.91[ASN][1000 genomes]
rs888635	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs918357	0.93[ASN][1000 genomes]
rs929734	0.89[ASN][1000 genomes]
rs959285	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs959286	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9808326	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
2	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
3	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:54302800-54317800	Weak transcription	Left Ventricle	heart
5	chr2:54305400-54321600	Weak transcription	Lung	lung
6	chr2:54307400-54319400	Weak transcription	Primary T cells from cord blood	blood
7	chr2:54309000-54317600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:54311000-54317800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:54311000-54317800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:54311000-54324200	Weak transcription	HSMMtube	muscle
11	chr2:54311800-54317600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:54314800-54316200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:54315000-54315800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:54315000-54315800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:54315000-54315800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:54315000-54316000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:54315000-54316000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:54315000-54316000	Enhancers	Adipose Nuclei	Adipose
19	chr2:54315000-54316000	Enhancers	HMEC	breast
20	chr2:54315000-54316800	Enhancers	HepG2	liver
21	chr2:54315000-54317000	Enhancers	Fetal Intestine Large	intestine
22	chr2:54315000-54317000	Enhancers	Fetal Intestine Small	intestine
23	chr2:54315200-54315800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:54315200-54315800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:54315200-54315800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:54315200-54315800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr2:54315200-54315800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:54315200-54315800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:54315200-54315800	Enhancers	Fetal Muscle Leg	muscle
30	chr2:54315200-54315800	Enhancers	Gastric	stomach
31	chr2:54315200-54315800	Enhancers	Pancreas	Pancrea
32	chr2:54315200-54315800	Enhancers	Right Atrium	heart
33	chr2:54315200-54316000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:54315200-54316000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:54315200-54316000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:54315200-54316000	Enhancers	NH-A	brain
37	chr2:54315200-54316200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:54315200-54316200	Enhancers	Stomach Mucosa	stomach
39	chr2:54315200-54316200	Enhancers	K562	blood
40	chr2:54315400-54315800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:54315400-54315800	Enhancers	Fetal Muscle Trunk	muscle
42	chr2:54315400-54315800	Enhancers	Fetal Stomach	stomach
43	chr2:54315400-54316200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:54315600-54315800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:54315600-54315800	Enhancers	Esophagus	oesophagus
46	chr2:54315600-54316000	Flanking Active TSS	NHEK	skin
47	chr2:54315600-54317800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:54315600-54319800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:54315600-54322600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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