Variant report

Variant	rs805274
Chromosome Location	chr6:31665194-31665195
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	chr6:31664975..31665752-chr6:31737286..31737856,2	K562	blood:
2	chr6:31663587..31667118-chr6:31669359..31672270,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204427	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1052486	0.86[ASN][1000 genomes]
rs1077393	0.86[ASN][1000 genomes]
rs1266075	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1266076	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2077491	0.84[ASN][1000 genomes]
rs2242659	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2242660	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2736155	0.83[ASN][1000 genomes]
rs2844465	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs385306	0.82[ASN][1000 genomes]
rs4569	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7029	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs707917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707920	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7992	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805257	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs805262	0.81[ASN][1000 genomes]
rs805271	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805277	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805282	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805285	0.82[ASN][1000 genomes]
rs805286	0.80[ASN][1000 genomes]
rs805287	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs805288	0.83[EUR][1000 genomes]
rs805290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805294	0.81[ASN][1000 genomes]
rs805301	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs805302	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs805303	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs813115	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
12	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
13	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
14	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs805274	CSNK2B	cis	lymphoblastoid	seeQTL
rs805274	BAT4	Cis_1M	lymphoblastoid	RTeQTL
rs805274	AIF1	Cis_1M	lymphoblastoid	RTeQTL
rs805274	GRM4	cis	cerebellum	SCAN
rs805274	LY6G5C	cis	Cerebellum	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31649600-31669400	Weak transcription	HMEC	breast
2	chr6:31650800-31668800	Strong transcription	Thymus	Thymus
3	chr6:31651200-31668600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:31651600-31667800	Strong transcription	Brain Germinal Matrix	brain
5	chr6:31651600-31668600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:31651800-31665400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:31651800-31669200	Weak transcription	Fetal Heart	heart
8	chr6:31652000-31665600	Strong transcription	Adipose Nuclei	Adipose
9	chr6:31652000-31668000	Strong transcription	Liver	Liver
10	chr6:31652000-31668600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:31652000-31668600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:31652000-31668600	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:31652000-31668600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr6:31652000-31668800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:31652200-31666000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:31652200-31666000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:31652200-31668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:31652200-31668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:31652200-31668600	Strong transcription	Fetal Stomach	stomach
20	chr6:31652200-31668800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr6:31652400-31665400	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:31652400-31668800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:31652600-31666000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:31653400-31667800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:31653600-31665400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:31653600-31665400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:31653600-31665600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:31653600-31665600	Strong transcription	Primary T cells from cord blood	blood
29	chr6:31653600-31667200	Strong transcription	Lung	lung
30	chr6:31653600-31668000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:31653600-31668600	Strong transcription	Fetal Muscle Leg	muscle
32	chr6:31653800-31665600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:31653800-31665800	Strong transcription	Brain Cingulate Gyrus	brain
34	chr6:31653800-31665800	Strong transcription	Brain Substantia Nigra	brain
35	chr6:31653800-31665800	Strong transcription	Colon Smooth Muscle	Colon
36	chr6:31653800-31665800	Strong transcription	Fetal Brain Female	brain
37	chr6:31653800-31666800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:31653800-31668000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:31654000-31665400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:31654000-31665600	Strong transcription	Rectal Smooth Muscle	rectum
41	chr6:31654000-31665800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr6:31654000-31666600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr6:31654000-31668000	Strong transcription	Left Ventricle	heart
44	chr6:31654000-31668200	Strong transcription	Dnd41	blood
45	chr6:31654000-31668400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:31654000-31669000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:31654200-31665600	Strong transcription	Fetal Lung	lung
48	chr6:31654200-31668800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:31654600-31668600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:31656600-31665800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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