Variant report

Variant	rs72834621
Chromosome Location	chr6:26005023-26005024
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25995733..25998367-chr6:26002455..26005186,2	MCF-7	breast:
2	chr6:26004960..26009500-chr6:26017429..26023147,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM38-1	chr6:25998131-26012068	NONHSAT108196

Variant related genes	Relation type
ENSG00000124610	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000198366	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1836859	1.00[AFR][1000 genomes]
rs3799369	1.00[AFR][1000 genomes]
rs72832571	0.86[AFR][1000 genomes]
rs72832583	1.00[AFR][1000 genomes]
rs72832588	1.00[AFR][1000 genomes]
rs72832593	1.00[AFR][1000 genomes]
rs72832602	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72834627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72834630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72834642	0.84[AMR][1000 genomes]
rs72834643	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72834647	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7752351	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7766267	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription 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 miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases
8	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
9	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
11	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
12	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
13	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 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	chr6:25993400-26007400	Weak transcription	Small Intestine	intestine
2	chr6:25993600-26005800	Weak transcription	HSMM	muscle
3	chr6:25993600-26005800	Weak transcription	HSMMtube	muscle
4	chr6:25993600-26006000	Weak transcription	Brain Substantia Nigra	brain
5	chr6:25993600-26006400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:25993600-26007400	Weak transcription	Brain Angular Gyrus	brain
7	chr6:25993600-26011200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:25993600-26015800	Weak transcription	Fetal Kidney	kidney
9	chr6:25993600-26016600	Weak transcription	Aorta	Aorta
10	chr6:25993800-26016400	Weak transcription	NHLF	lung
11	chr6:25994000-26006400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:25994000-26006400	Weak transcription	HUVEC	blood vessel
13	chr6:25994200-26006400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:25997800-26006400	Weak transcription	K562	blood
15	chr6:25998600-26008600	Weak transcription	Psoas Muscle	Psoas
16	chr6:25998600-26009200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:25999000-26006800	Weak transcription	Primary T cells from cord blood	blood
18	chr6:25999000-26007800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:25999000-26010000	Weak transcription	Primary B cells from cord blood	blood
20	chr6:25999200-26006400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:25999200-26006400	Weak transcription	Lung	lung
22	chr6:25999200-26007400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:25999200-26016400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:25999200-26016600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:25999200-26016600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:25999200-26017200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:25999400-26005600	Weak transcription	Dnd41	blood
28	chr6:25999400-26006600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:25999400-26008000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:25999400-26009800	Weak transcription	Gastric	stomach
31	chr6:25999400-26016400	Weak transcription	Right Ventricle	heart
32	chr6:25999400-26016600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:25999400-26016600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:25999400-26016600	Weak transcription	Pancreas	Pancrea
35	chr6:25999400-26017400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:25999600-26006400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:25999600-26006600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:25999600-26006800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:25999600-26007600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr6:25999600-26008600	Weak transcription	Spleen	Spleen
41	chr6:25999600-26016800	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:25999800-26016600	Weak transcription	Esophagus	oesophagus
43	chr6:26001200-26008200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:26001200-26016800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr6:26001400-26006200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:26001400-26006400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:26001400-26006800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:26001400-26015800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:26001600-26016000	Weak transcription	Liver	Liver
50	chr6:26001600-26016400	Weak transcription	Fetal Intestine Large	intestine

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