Variant report

Variant	rs9465657
Chromosome Location	chr6:20202237-20202238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:20199968..20202569-chr6:20401397..20403351,2	MCF-7	breast:
2	chr6:20199925..20202970-chr6:20211369..20213429,3	MCF-7	breast:
3	chr6:20201447..20207053-chr6:20401187..20404960,5	K562	blood:
4	chr6:20198875..20206310-chr6:20399680..20405305,15	K562	blood:
5	chr6:20180103..20182906-chr6:20201581..20203746,2	K562	blood:

Variant related genes	Relation type
ENSG00000112242	Chromatin interaction
ENSG00000172197	Chromatin interaction
ENSG00000227803	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs4710923	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55948432	0.94[ASN][1000 genomes]
rs6456303	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6907076	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6908738	0.94[ASN][1000 genomes]
rs6911788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6928994	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6935894	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9465654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9465655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9465656	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[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	nsv1029729	chr6:20113226-20235122	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538155	chr6:20113226-20235122	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1033904	chr6:20127596-20210374	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1799840	chr6:20196549-20210374	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:20175000-20205200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:20182000-20204400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:20183600-20204200	Weak transcription	Right Atrium	heart
4	chr6:20184400-20202400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:20187600-20204400	Weak transcription	Lung	lung
6	chr6:20187800-20203000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:20193000-20209200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:20193200-20204200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:20193200-20204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:20197400-20202400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:20197800-20204400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:20198600-20206400	Enhancers	Colon Smooth Muscle	Colon
13	chr6:20199200-20202600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:20199200-20204200	Weak transcription	Colonic Mucosa	Colon
15	chr6:20199400-20206000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:20199400-20207600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:20199400-20210000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:20199600-20204200	Weak transcription	Adipose Nuclei	Adipose
19	chr6:20199600-20207600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr6:20199800-20204200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:20200400-20203200	Enhancers	Fetal Kidney	kidney
22	chr6:20200400-20205000	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr6:20200600-20206200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:20200600-20209200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr6:20200800-20202400	Enhancers	A549	lung
26	chr6:20200800-20202400	Enhancers	K562	blood
27	chr6:20200800-20204400	Enhancers	Fetal Heart	heart
28	chr6:20200800-20204400	Enhancers	Hela-S3	cervix
29	chr6:20201000-20202400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:20201000-20203200	Enhancers	NHDF-Ad	bronchial
31	chr6:20201000-20203400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr6:20201000-20206000	Enhancers	Duodenum Mucosa	Duodenum
33	chr6:20201200-20202400	Enhancers	NHEK	skin
34	chr6:20201200-20204400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:20201200-20204400	Weak transcription	Gastric	stomach
36	chr6:20201200-20205000	Enhancers	Fetal Intestine Small	intestine
37	chr6:20201200-20205000	Enhancers	Dnd41	blood
38	chr6:20201200-20205400	Enhancers	Fetal Intestine Large	intestine
39	chr6:20201200-20205800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:20201200-20205800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:20201200-20206000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr6:20201200-20206000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:20201200-20206800	Enhancers	Primary hematopoietic stem cells	blood
44	chr6:20201200-20207000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:20201400-20202400	Enhancers	Small Intestine	intestine
46	chr6:20201400-20202600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr6:20201400-20202600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:20201400-20204200	Weak transcription	Right Ventricle	heart
49	chr6:20201400-20204400	Weak transcription	Esophagus	oesophagus
50	chr6:20201400-20204400	Weak transcription	Fetal Muscle Leg	muscle

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