Variant report

Variant	rs6478305
Chromosome Location	chr9:100375204-100375205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100371781..100375300-chr9:100375938..100379259,4	K562	blood:
2	chr9:100371928..100375283-chr9:100389533..100393733,3	K562	blood:

Variant related genes	Relation type
ENSG00000136925	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1034098	0.86[AFR][1000 genomes]
rs1116208	0.86[AFR][1000 genomes]
rs14066	0.86[AFR][1000 genomes]
rs1411344	0.86[AFR][1000 genomes]
rs1543636	0.80[YRI][hapmap];0.85[AFR][1000 genomes]
rs16923033	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16923041	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs1813875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1928641	0.80[YRI][hapmap];0.86[AFR][1000 genomes]
rs1928642	0.86[AFR][1000 genomes]
rs2282066	0.86[AFR][1000 genomes]
rs2282067	0.85[AFR][1000 genomes]
rs2297155	0.80[YRI][hapmap]
rs2297156	0.80[YRI][hapmap]
rs2297158	0.80[YRI][hapmap]
rs2297159	0.80[YRI][hapmap]
rs2297160	0.80[YRI][hapmap]
rs2401635	0.80[YRI][hapmap]
rs28403588	0.82[AFR][1000 genomes]
rs28403589	0.83[AFR][1000 genomes]
rs3176635	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3176637	0.80[YRI][hapmap]
rs3176638	0.80[YRI][hapmap]
rs3176644	0.80[YRI][hapmap]
rs3176651	0.80[YRI][hapmap]
rs3176657	0.87[AFR][1000 genomes]
rs3176659	0.80[YRI][hapmap]
rs3176670	0.80[YRI][hapmap]
rs3176675	0.86[YRI][hapmap]
rs3176682	0.80[YRI][hapmap]
rs3176685	0.80[YRI][hapmap]
rs3176687	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176688	0.80[YRI][hapmap]
rs3176706	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176708	0.83[YRI][hapmap]
rs3176711	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176712	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176714	0.80[YRI][hapmap]
rs3176720	0.80[YRI][hapmap]
rs3176723	0.80[YRI][hapmap]
rs3176724	0.80[YRI][hapmap]
rs3176726	0.80[YRI][hapmap]
rs3750370	0.86[AFR][1000 genomes]
rs3802472	0.86[AFR][1000 genomes]
rs3802473	0.86[AFR][1000 genomes]
rs3802474	0.80[YRI][hapmap]
rs41274252	0.86[AFR][1000 genomes]
rs55966848	0.85[AFR][1000 genomes]
rs56060429	0.85[AFR][1000 genomes]
rs58146508	0.81[AFR][1000 genomes]
rs58387091	0.86[AFR][1000 genomes]
rs58390229	0.84[AFR][1000 genomes]
rs58637778	0.86[AFR][1000 genomes]
rs58878935	0.83[AFR][1000 genomes]
rs59478543	0.85[AFR][1000 genomes]
rs59662386	0.81[AFR][1000 genomes]
rs59791764	0.85[AFR][1000 genomes]
rs59992945	0.86[AFR][1000 genomes]
rs60026475	0.84[AFR][1000 genomes]
rs60028882	0.86[AFR][1000 genomes]
rs60055057	0.81[AFR][1000 genomes]
rs60596698	0.86[AFR][1000 genomes]
rs60653177	0.86[AFR][1000 genomes]
rs61221847	0.81[AFR][1000 genomes]
rs61276200	0.85[AFR][1000 genomes]
rs61445476	0.85[AFR][1000 genomes]
rs61739366	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6478304	0.80[YRI][hapmap];0.86[AFR][1000 genomes]
rs7018546	0.85[AFR][1000 genomes]
rs7021377	0.89[AFR][1000 genomes]
rs7025403	0.86[AFR][1000 genomes]
rs7036604	0.80[YRI][hapmap];0.86[AFR][1000 genomes]
rs7049183	0.85[AFR][1000 genomes]
rs7341850	0.81[AFR][1000 genomes]
rs73498323	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498324	0.83[AFR][1000 genomes]
rs73498329	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498332	0.81[AFR][1000 genomes]
rs73498338	0.81[AFR][1000 genomes]
rs73498347	0.81[AFR][1000 genomes]
rs73498348	0.81[AFR][1000 genomes]
rs73498355	0.81[AFR][1000 genomes]
rs73498358	0.81[AFR][1000 genomes]
rs73498359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498362	0.81[AFR][1000 genomes]
rs73498365	0.89[AFR][1000 genomes]
rs73500307	0.88[AFR][1000 genomes]
rs73500321	0.89[AFR][1000 genomes]
rs73500392	0.88[AFR][1000 genomes]
rs73502208	0.87[AFR][1000 genomes]
rs73502210	0.87[AFR][1000 genomes]
rs73551090	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73552520	0.85[AFR][1000 genomes]
rs73554631	0.85[AFR][1000 genomes]
rs73554641	0.86[AFR][1000 genomes]
rs73554646	0.86[AFR][1000 genomes]
rs73554650	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73554652	0.86[AFR][1000 genomes]
rs7856316	0.86[AFR][1000 genomes]
rs7857174	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7859684	0.86[AFR][1000 genomes]
rs7859979	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7866961	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs7867046	0.80[YRI][hapmap];0.86[AFR][1000 genomes]
rs7869683	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100348800-100384000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:100361000-100381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:100361600-100375800	Strong transcription	Primary B cells from peripheral blood	blood
4	chr9:100361800-100375800	Strong transcription	Primary T cells from cord blood	blood
5	chr9:100361800-100376000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:100361800-100376000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr9:100361800-100376000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:100361800-100376000	Strong transcription	Duodenum Mucosa	Duodenum
9	chr9:100361800-100383400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:100361800-100389000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:100361800-100394000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:100362200-100379000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:100362400-100376400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:100362400-100376400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:100362600-100376000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:100363000-100394600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:100365200-100375600	Strong transcription	Left Ventricle	heart
18	chr9:100365200-100382200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:100365800-100389400	Weak transcription	Stomach Mucosa	stomach
20	chr9:100367400-100386200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:100367400-100387000	Weak transcription	HMEC	breast
22	chr9:100367600-100377000	Weak transcription	NHEK	skin
23	chr9:100367600-100384000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:100367600-100390400	Weak transcription	Small Intestine	intestine
25	chr9:100367800-100383800	Weak transcription	A549	lung
26	chr9:100367800-100384000	Weak transcription	Aorta	Aorta
27	chr9:100367800-100384400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:100368200-100379400	Weak transcription	Gastric	stomach
29	chr9:100368200-100380400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr9:100368200-100386200	Weak transcription	Esophagus	oesophagus
31	chr9:100368200-100394000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:100368200-100394200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr9:100368400-100379800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:100368400-100379800	Weak transcription	Right Ventricle	heart
35	chr9:100368400-100384000	Weak transcription	Pancreas	Pancrea
36	chr9:100368400-100387800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:100368400-100394000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:100368600-100379800	Weak transcription	Hela-S3	cervix
39	chr9:100369000-100378600	Weak transcription	NHLF	lung
40	chr9:100369000-100386400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:100369000-100388200	Strong transcription	Fetal Muscle Leg	muscle
42	chr9:100369200-100377400	Weak transcription	Fetal Heart	heart
43	chr9:100369600-100382600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr9:100370800-100376200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr9:100370800-100379400	Strong transcription	Fetal Thymus	thymus
46	chr9:100371000-100376200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr9:100371000-100382400	Weak transcription	Fetal Intestine Small	intestine
48	chr9:100371200-100382800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:100371800-100375800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:100371800-100376600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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