Variant report

Variant	rs6541092
Chromosome Location	chr1:10441978-10441979
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10440159..10442885-chr1:10447718..10449584,2	MCF-7	breast:
2	chr1:10439520..10442489-chr1:10444058..10446995,2	MCF-7	breast:
3	chr1:10438971..10445404-chr1:10456959..10461376,9	MCF-7	breast:
4	chr1:10440809..10443662-chr1:10447796..10449625,2	MCF-7	breast:
5	chr1:10440249..10443281-chr1:10456910..10459943,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DFFA-2	chr1:10441734-10442604	expReg_chr1_1471_-

Variant related genes	Relation type
ENSG00000142657	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10864454	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11121542	0.85[EUR][1000 genomes]
rs11121548	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12120465	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12125492	0.85[EUR][1000 genomes]
rs12135219	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12135774	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12141192	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12142043	0.85[EUR][1000 genomes]
rs3762289	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4240912	0.87[EUR][1000 genomes]
rs4240913	0.87[EUR][1000 genomes]
rs4846214	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4846215	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4846217	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58036267	0.81[AMR][1000 genomes]
rs61383940	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6670157	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6679596	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6693965	0.83[AMR][1000 genomes]
rs6694081	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6703602	0.83[AMR][1000 genomes]
rs7525661	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS 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	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6541092	KIF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10393800-10444600	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:10400600-10446400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:10400600-10447400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:10409800-10447400	Weak transcription	Small Intestine	intestine
5	chr1:10418400-10445600	Strong transcription	Fetal Brain Female	brain
6	chr1:10419200-10442800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:10420200-10445000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:10420200-10446000	Strong transcription	Brain Germinal Matrix	brain
9	chr1:10422400-10447200	Weak transcription	Fetal Heart	heart
10	chr1:10425800-10447800	Weak transcription	Psoas Muscle	Psoas
11	chr1:10428400-10442000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:10430400-10443800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:10431200-10444800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:10433400-10442000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:10434400-10447400	Weak transcription	HMEC	breast
16	chr1:10435400-10447800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:10435400-10448000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:10435600-10443200	Weak transcription	Fetal Brain Male	brain
19	chr1:10435600-10444400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:10435600-10447400	Weak transcription	Aorta	Aorta
21	chr1:10435600-10447600	Weak transcription	Thymus	Thymus
22	chr1:10435600-10448800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:10435600-10448800	Weak transcription	Gastric	stomach
24	chr1:10435800-10448000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:10436800-10448400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:10437000-10447800	Weak transcription	Left Ventricle	heart
27	chr1:10437000-10448000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:10437400-10447000	Weak transcription	Dnd41	blood
29	chr1:10437400-10447600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:10437600-10442000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:10437600-10443600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:10437600-10447800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:10438600-10445800	Strong transcription	Fetal Muscle Leg	muscle
34	chr1:10438600-10447000	Weak transcription	Primary B cells from cord blood	blood
35	chr1:10438600-10458200	Weak transcription	Right Atrium	heart
36	chr1:10438800-10445400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:10438800-10445400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:10438800-10446400	Weak transcription	Hela-S3	cervix
39	chr1:10438800-10447600	Weak transcription	Fetal Kidney	kidney
40	chr1:10438800-10448000	Weak transcription	Spleen	Spleen
41	chr1:10439000-10447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:10439000-10448200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:10439200-10447200	Weak transcription	Fetal Lung	lung
44	chr1:10439200-10447200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:10439200-10447600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:10439400-10446400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:10439400-10447000	Weak transcription	Fetal Thymus	thymus
48	chr1:10439400-10447000	Weak transcription	NHEK	skin
49	chr1:10439400-10447400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:10439600-10445200	Weak transcription	HepG2	liver

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