Variant report

Variant	rs72934664
Chromosome Location	chr3:98539860-98539861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:98539802-98540264	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:98539036-98544468	U87	brain:	n/a	n/a
3	POLR2A	chr3:98532422-98540691	U87	brain:	n/a	n/a
4	POLR2A	chr3:98531678-98540691	U87	brain:	n/a	n/a
5	POLR2A	chr3:98539030-98544468	U87	brain:	n/a	n/a
6	TCF12	chr3:98539830-98540422	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST3GAL6-3	chr3:98539632-98540045	NONHSAT090824

Variant related genes	Relation type
DCBLD2	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs13085453	1.00[AMR][1000 genomes]
rs56996908	1.00[AMR][1000 genomes]
rs57492353	1.00[AMR][1000 genomes]
rs57581846	1.00[AMR][1000 genomes]
rs58345395	1.00[AMR][1000 genomes]
rs58880987	1.00[AMR][1000 genomes]
rs58977425	1.00[AMR][1000 genomes]
rs58988785	1.00[AMR][1000 genomes]
rs59462320	1.00[AMR][1000 genomes]
rs59581962	1.00[AMR][1000 genomes]
rs59726038	1.00[AMR][1000 genomes]
rs60266120	1.00[AMR][1000 genomes]
rs60488063	1.00[AMR][1000 genomes]
rs61133181	1.00[AMR][1000 genomes]
rs61172524	1.00[AMR][1000 genomes]
rs61517408	1.00[AMR][1000 genomes]
rs72923005	1.00[AMR][1000 genomes]
rs72923016	1.00[AMR][1000 genomes]
rs72923020	1.00[AMR][1000 genomes]
rs72923040	1.00[AMR][1000 genomes]
rs72923043	1.00[AMR][1000 genomes]
rs72923045	1.00[AMR][1000 genomes]
rs72923046	1.00[AMR][1000 genomes]
rs72923053	1.00[AMR][1000 genomes]
rs72923071	1.00[AMR][1000 genomes]
rs72925007	1.00[AMR][1000 genomes]
rs72925011	1.00[AMR][1000 genomes]
rs72934627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934633	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934639	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934644	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934650	1.00[AMR][1000 genomes]
rs72934662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934681	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936622	1.00[AMR][1000 genomes]
rs72936644	1.00[AMR][1000 genomes]
rs72936652	1.00[AMR][1000 genomes]
rs72936657	1.00[AMR][1000 genomes]
rs72936667	1.00[AMR][1000 genomes]
rs72936668	1.00[AMR][1000 genomes]
rs72938539	1.00[AMR][1000 genomes]
rs72938573	1.00[AMR][1000 genomes]
rs72938584	1.00[AMR][1000 genomes]
rs72938585	1.00[AMR][1000 genomes]
rs72940515	1.00[AMR][1000 genomes]
rs72940521	1.00[AMR][1000 genomes]
rs72940528	1.00[AMR][1000 genomes]
rs72940538	1.00[AMR][1000 genomes]
rs72940543	1.00[AMR][1000 genomes]
rs72940552	1.00[AMR][1000 genomes]
rs72940570	1.00[AMR][1000 genomes]
rs72940573	1.00[AMR][1000 genomes]
rs72940576	1.00[AMR][1000 genomes]
rs72940577	1.00[AMR][1000 genomes]
rs72940581	1.00[AMR][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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
3	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:98524200-98544200	Strong transcription	HSMM	muscle
6	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
7	chr3:98526200-98543200	Weak transcription	Lung	lung
8	chr3:98526400-98542800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:98526400-98544200	Weak transcription	Brain Angular Gyrus	brain
10	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
11	chr3:98526600-98540000	Weak transcription	Fetal Thymus	thymus
12	chr3:98527200-98542200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:98527200-98545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:98527200-98545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:98528400-98542200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:98528600-98543600	Strong transcription	NHEK	skin
18	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:98529000-98540000	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:98529400-98546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:98530400-98542000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:98530800-98542600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:98532400-98541200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:98532400-98546200	Weak transcription	Esophagus	oesophagus
25	chr3:98532800-98541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:98534000-98545000	Weak transcription	Ovary	ovary
27	chr3:98534000-98552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:98534200-98542800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:98534200-98552200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:98534400-98545600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:98534600-98544200	Strong transcription	HMEC	breast
32	chr3:98534600-98545600	Weak transcription	Fetal Intestine Small	intestine
33	chr3:98535200-98540200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:98535400-98541800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:98535400-98542600	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr3:98535400-98543800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:98535600-98541600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:98536000-98540400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:98536000-98542000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:98536000-98542800	Strong transcription	NH-A	brain
41	chr3:98536000-98552600	Weak transcription	Pancreas	Pancrea
42	chr3:98536200-98542600	Weak transcription	Fetal Intestine Large	intestine
43	chr3:98536200-98542600	Weak transcription	Fetal Stomach	stomach
44	chr3:98536200-98594200	Weak transcription	HepG2	liver
45	chr3:98536800-98543000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:98536800-98545000	Weak transcription	Fetal Kidney	kidney
47	chr3:98537000-98541400	Strong transcription	HUVEC	blood vessel
48	chr3:98537000-98542600	Weak transcription	Dnd41	blood
49	chr3:98537000-98542600	Strong transcription	Osteobl	bone
50	chr3:98537000-98545600	Weak transcription	HSMMtube	muscle

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