Variant report

Variant	rs9349843
Chromosome Location	chr6:56933942-56933943
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56911298..56913104-chr6:56932457..56934576,2	K562	blood:
2	chr6:56927166..56929779-chr6:56933810..56935740,2	K562	blood:
3	chr6:56927166..56931144-chr6:56933264..56935740,4	K562	blood:
4	chr6:56883885..56886114-chr6:56933093..56934957,2	K562	blood:
5	chr6:56932277..56934090-chr6:56953259..56955727,2	K562	blood:

Variant related genes	Relation type
ENSG00000168116	Chromatin interaction
ENSG00000112200	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1157713	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190416	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190434	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192711	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12210597	0.93[ASN][1000 genomes]
rs12211611	0.96[ASN][1000 genomes]
rs1901382	0.83[EUR][1000 genomes]
rs2100305	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2273921	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734738	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778515	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800019	0.93[ASN][1000 genomes]
rs3996929	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3996933	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3996937	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4715646	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6459180	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6913707	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6926980	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6928715	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6929783	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6936472	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743855	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7744316	0.93[ASN][1000 genomes]
rs7744824	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7753537	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753927	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7763570	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8180538	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9367704	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367708	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370564	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370565	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382689	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9396259	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952647	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885757	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1026524	chr6:56902544-56951703	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv970717	chr6:56903957-56955783	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv885913	chr6:56910884-56954439	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv970684	chr6:56912349-56953340	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	esv3374787	chr6:56912959-56955113	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	esv2763988	chr6:56913072-56952630	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv603189	chr6:56913453-56950609	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv538230	chr6:56913943-56951703	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv526143	chr6:56917538-56954439	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9349843	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs9349843	RAB23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56911600-56935200	Weak transcription	Gastric	stomach
2	chr6:56911600-56939800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:56911800-56934200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:56911800-56936200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:56911800-56943000	Weak transcription	Esophagus	oesophagus
6	chr6:56913400-56940600	Weak transcription	Brain Substantia Nigra	brain
7	chr6:56913600-56934000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:56913600-56941600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:56914000-56934600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:56914200-56934200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:56914400-56935000	Weak transcription	Fetal Kidney	kidney
12	chr6:56914600-56954200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:56915000-56940200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:56916800-56935400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:56916800-56935600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:56916800-56954400	Weak transcription	Thymus	Thymus
17	chr6:56917000-56934000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:56918200-56940400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:56918400-56936600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:56918400-56954200	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:56918800-56938600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:56921600-56938400	Weak transcription	Aorta	Aorta
23	chr6:56921600-56940600	Weak transcription	Fetal Intestine Large	intestine
24	chr6:56921600-56941200	Weak transcription	NHEK	skin
25	chr6:56923000-56937800	Weak transcription	Right Ventricle	heart
26	chr6:56925200-56934000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:56925200-56939600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:56925200-56941800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:56925400-56934200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:56925400-56941400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:56925400-56942200	Weak transcription	HSMMtube	muscle
32	chr6:56925400-56954400	Weak transcription	Primary B cells from cord blood	blood
33	chr6:56925600-56934000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:56925600-56954200	Weak transcription	Hela-S3	cervix
35	chr6:56926400-56944600	Weak transcription	Pancreas	Pancrea
36	chr6:56926600-56954200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:56927000-56935000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:56927000-56938600	Weak transcription	Ovary	ovary
39	chr6:56927000-56954800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:56927200-56954000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:56927400-56934000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:56927400-56940800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr6:56928600-56938000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:56929200-56954200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:56929400-56954200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:56929800-56944800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:56930000-56940400	Weak transcription	NHLF	lung
48	chr6:56930000-56941800	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:56930000-56943200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr6:56930000-56950000	Weak transcription	NHDF-Ad	bronchial

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