Variant report

Variant	rs6006239
Chromosome Location	chr22:30150320-30150321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30149066..30150867-chr22:30154689..30156736,2	K562	blood:
2	chr22:30148345..30151530-chr22:30155464..30158156,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200976	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1001318	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12158466	0.82[EUR][1000 genomes]
rs12159536	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12163073	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12627866	0.87[AFR][1000 genomes]
rs12628545	1.00[CEU][hapmap]
rs13057811	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs14115	0.82[EUR][1000 genomes]
rs2018808	0.82[EUR][1000 genomes]
rs2232903	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28730892	0.82[EUR][1000 genomes]
rs5997507	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs5997508	0.89[ASN][1000 genomes]
rs5997509	0.89[ASN][1000 genomes]
rs5997515	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997518	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997519	0.82[EUR][1000 genomes]
rs5997520	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs5997524	0.82[EUR][1000 genomes]
rs6006234	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6006235	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6006238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006241	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006247	0.82[EUR][1000 genomes]
rs6006249	0.82[EUR][1000 genomes]
rs6006250	0.82[EUR][1000 genomes]
rs6006262	0.82[EUR][1000 genomes]
rs60102307	0.97[EUR][1000 genomes]
rs71331211	0.89[ASN][1000 genomes]
rs7285660	0.82[EUR][1000 genomes]
rs7285800	0.82[EUR][1000 genomes]
rs7290420	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73392899	0.88[AFR][1000 genomes]
rs73394838	0.82[EUR][1000 genomes]
rs8138165	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1065072	chr22:30102176-30155245	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30130400-30150600	Strong transcription	Fetal Intestine Small	intestine
2	chr22:30131600-30162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:30134400-30158400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr22:30136000-30154800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr22:30141200-30150800	Strong transcription	Fetal Brain Female	brain
6	chr22:30141600-30154200	Weak transcription	Osteobl	bone
7	chr22:30141800-30155400	Strong transcription	Fetal Stomach	stomach
8	chr22:30143600-30154200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr22:30144400-30161800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr22:30144400-30162000	Weak transcription	Placenta	Placenta
11	chr22:30144400-30162200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr22:30144600-30160000	Weak transcription	Dnd41	blood
13	chr22:30144600-30161800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr22:30144600-30161800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr22:30144600-30161800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr22:30144600-30162000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr22:30144800-30155000	Weak transcription	Ovary	ovary
18	chr22:30144800-30161800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr22:30144800-30161800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr22:30144800-30161800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr22:30145200-30154000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr22:30145400-30154200	Weak transcription	NHDF-Ad	bronchial
23	chr22:30146000-30150800	Strong transcription	Primary T cells from cord blood	blood
24	chr22:30146000-30161800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr22:30146400-30155000	Weak transcription	Brain Substantia Nigra	brain
26	chr22:30146600-30154800	Weak transcription	Left Ventricle	heart
27	chr22:30146600-30161800	Weak transcription	Brain Germinal Matrix	brain
28	chr22:30146800-30151800	Weak transcription	Esophagus	oesophagus
29	chr22:30146800-30151800	Weak transcription	NHLF	lung
30	chr22:30146800-30153400	Weak transcription	Aorta	Aorta
31	chr22:30146800-30154800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr22:30146800-30161800	Weak transcription	Brain Anterior Caudate	brain
33	chr22:30146800-30161800	Weak transcription	Right Ventricle	heart
34	chr22:30147000-30162000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr22:30147000-30162200	Weak transcription	Gastric	stomach
36	chr22:30147400-30152200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr22:30147400-30154000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr22:30147400-30160200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr22:30147400-30160200	Weak transcription	HepG2	liver
40	chr22:30147400-30161800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr22:30147600-30161800	Weak transcription	Primary B cells from cord blood	blood
42	chr22:30147600-30161800	Weak transcription	NHEK	skin
43	chr22:30147600-30162200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr22:30147800-30150400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr22:30147800-30150800	Weak transcription	GM12878-XiMat	blood
46	chr22:30147800-30153600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr22:30147800-30160200	Weak transcription	Fetal Thymus	thymus
48	chr22:30147800-30160800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr22:30147800-30161800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr22:30148000-30150400	Strong transcription	Brain Inferior Temporal Lobe	brain

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