Variant report

Variant	rs4959668
Chromosome Location	chr6:2449614-2449615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:2448542-2449748	SK-N-SH	brain:	n/a	chr6:2449162-2449181
2	CREB1	chr6:2448918-2449648	H1-hESC	embryonic stem cell:	n/a	chr6:2449417-2449430 chr6:2449417-2449430
3	CTCF	chr6:2449560-2449710	HUVEC	blood vessel:	n/a	n/a
4	CTCF	chr6:2449500-2449650	GM12872	blood:	n/a	n/a
5	E2F6	chr6:2449025-2449723	H1-hESC	embryonic stem cell:	n/a	chr6:2449418-2449427 chr6:2449420-2449429
6	CREB1	chr6:2449047-2449623	H1-hESC	embryonic stem cell:	n/a	chr6:2449417-2449430 chr6:2449417-2449430

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:2353810..2354693-chr6:2448790..2449627,3	MCF-7	breast:
2	chr6:2209266..2210149-chr6:2448969..2449652,2	MCF-7	breast:

Variant related genes	Relation type
GMDS-AS1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12529088	0.80[CEU][hapmap]
rs13194198	0.83[EUR][1000 genomes]
rs13198172	0.90[EUR][1000 genomes]
rs17135028	0.83[EUR][1000 genomes]
rs17536894	0.92[EUR][1000 genomes]
rs17608626	0.80[CEU][hapmap]
rs17609498	0.93[EUR][1000 genomes]
rs2073004	0.83[EUR][1000 genomes]
rs34077848	0.85[EUR][1000 genomes]
rs34610626	0.92[EUR][1000 genomes]
rs34854900	0.88[EUR][1000 genomes]
rs34901328	0.92[EUR][1000 genomes]
rs34996746	0.90[EUR][1000 genomes]
rs35182831	0.93[EUR][1000 genomes]
rs35658601	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35892674	0.92[EUR][1000 genomes]
rs35918040	0.85[EUR][1000 genomes]
rs3734504	0.80[CEU][hapmap]
rs3734505	0.81[CEU][hapmap]
rs4959184	0.83[EUR][1000 genomes]
rs4959663	0.80[CEU][hapmap]
rs4959669	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55939357	0.89[EUR][1000 genomes]
rs56343276	0.92[EUR][1000 genomes]
rs59493792	0.92[EUR][1000 genomes]
rs6911665	0.80[CEU][hapmap]
rs71552124	0.93[EUR][1000 genomes]
rs9501836	0.80[CEU][hapmap]
rs9503185	0.80[CEU][hapmap]

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	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2414600-2452000	Weak transcription	Ovary	ovary
2	chr6:2417600-2454200	Weak transcription	Pancreas	Pancrea
3	chr6:2448400-2450000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:2448600-2449800	Enhancers	Fetal Brain Male	brain
5	chr6:2448600-2451400	Enhancers	Hela-S3	cervix
6	chr6:2448800-2450000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:2449200-2449800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr6:2449200-2449800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:2449200-2449800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:2449200-2449800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:2449200-2449800	Flanking Active TSS	Fetal Intestine Large	intestine
12	chr6:2449200-2450000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr6:2449200-2450200	Enhancers	Brain Hippocampus Middle	brain
14	chr6:2449400-2449800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:2449400-2449800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:2449400-2449800	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr6:2449400-2451200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:2449600-2449800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:2449600-2449800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:2449600-2449800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr6:2449600-2449800	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:2449600-2449800	Enhancers	Primary hematopoietic stem cells	blood
23	chr6:2449600-2449800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:2449600-2449800	Enhancers	Aorta	Aorta
25	chr6:2449600-2449800	Enhancers	Brain Angular Gyrus	brain
26	chr6:2449600-2449800	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:2449600-2449800	Enhancers	Fetal Intestine Small	intestine
28	chr6:2449600-2449800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr6:2449600-2449800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr6:2449600-2449800	Enhancers	A549	lung
31	chr6:2449600-2449800	Bivalent Enhancer	Osteobl	bone
32	chr6:2449600-2450200	Enhancers	Brain Anterior Caudate	brain
33	chr6:2449600-2450200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr6:2449600-2450200	Enhancers	Brain Substantia Nigra	brain
35	chr6:2449600-2450600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:2449600-2450600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:2449600-2450600	Weak transcription	Left Ventricle	heart
38	chr6:2449600-2451000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:2449600-2451000	Weak transcription	Adipose Nuclei	Adipose
40	chr6:2449600-2451000	Enhancers	HMEC	breast
41	chr6:2449600-2451600	Weak transcription	HepG2	liver
42	chr6:2449600-2452400	Enhancers	Fetal Heart	heart
43	chr6:2449600-2454600	Weak transcription	Fetal Kidney	kidney
44	chr6:2449600-2455800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:2449600-2460400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:2449600-2460400	Weak transcription	Fetal Brain Female	brain
47	chr6:2449600-2461200	Weak transcription	Stomach Smooth Muscle	stomach

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