Variant report

Variant	rs12734915
Chromosome Location	chr1:158983811-158983812
allele	A/C
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	chr1:158982898-158984553	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:158982037-158984384	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:158983699-158984460	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:158982888-158984463	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:158983414-158985843	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:158983215-158984375	U87	brain:	n/a	n/a
7	POLR2A	chr1:158981852-158987235	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:158978464-158986840	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:158983811-158984386	GM12891	blood:	n/a	n/a
10	CHD1	chr1:158981505-158983902	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:158983798-158984362	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:158983290-158984427	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:158981523-158987265	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:158983733-158984535	U87	brain:	n/a	n/a
15	POLR2A	chr1:158978384-158985943	GM19193	blood:	n/a	n/a
16	POLR2A	chr1:158983676-158984310	GM12891	blood:	n/a	n/a
17	POLR2A	chr1:158983209-158984552	U87	brain:	n/a	n/a
18	POLR2A	chr1:158983768-158984190	GM12891	blood:	n/a	n/a
19	POLR2A	chr1:158981580-158990399	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:158983734-158984416	GM12892	blood:	n/a	n/a
21	POLR2A	chr1:158981297-158987303	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:158978350-158987224	GM18505	blood:	n/a	n/a
23	POLR2A	chr1:158978475-158987184	GM19099	blood:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11539423	0.88[AMR][1000 genomes]
rs12728586	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12738378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12739704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12755219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16841500	0.88[AMR][1000 genomes]
rs1956	0.88[AMR][1000 genomes]
rs4262539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66519738	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72704976	0.88[AMR][1000 genomes]
rs7526724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs856047	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158976000-159000800	Weak transcription	Gastric	stomach
2	chr1:158977200-158990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:158978600-158984200	Active TSS	Rectal Smooth Muscle	rectum
4	chr1:158978800-158985800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:158979200-158984000	Active TSS	Stomach Smooth Muscle	stomach
6	chr1:158979400-158984000	Active TSS	Brain Hippocampus Middle	brain
7	chr1:158979400-158984000	Active TSS	GM12878-XiMat	blood
8	chr1:158979400-158984400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:158979400-158984400	Active TSS	Brain Anterior Caudate	brain
10	chr1:158979400-158984400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr1:158979800-158984600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:158981200-158985400	Weak transcription	Fetal Intestine Small	intestine
14	chr1:158981200-158985400	Weak transcription	Pancreas	Pancrea
15	chr1:158981200-158986400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:158981600-158984200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:158981600-158986000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr1:158982000-158984000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr1:158982000-158988000	Weak transcription	Fetal Brain Male	brain
20	chr1:158982200-158984200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:158982600-158984000	Weak transcription	Fetal Lung	lung
22	chr1:158982600-158984000	Active TSS	Left Ventricle	heart
23	chr1:158982600-158984000	Weak transcription	HSMMtube	muscle
24	chr1:158982600-158984400	Active TSS	Brain Substantia Nigra	brain
25	chr1:158982600-158984800	Strong transcription	HSMM	muscle
26	chr1:158982600-158985400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:158982600-158985400	Weak transcription	Brain Angular Gyrus	brain
28	chr1:158982600-158985400	Weak transcription	Fetal Stomach	stomach
29	chr1:158982600-158986200	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
31	chr1:158982800-158984400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:158982800-158984400	Weak transcription	Fetal Intestine Large	intestine
33	chr1:158982800-158984600	Weak transcription	NHLF	lung
34	chr1:158982800-158984800	Weak transcription	HMEC	breast
35	chr1:158982800-158985000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:158982800-158985200	Weak transcription	Stomach Mucosa	stomach
37	chr1:158982800-158985400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:158982800-158985400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:158982800-158985400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:158982800-158985400	Weak transcription	NH-A	brain
41	chr1:158982800-158987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:158982800-158989600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:158982800-159000200	Weak transcription	Aorta	Aorta
44	chr1:158983000-158984000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
45	chr1:158983000-158984200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr1:158983000-158984200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:158983000-158984200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:158983000-158984400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:158983000-158984400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
50	chr1:158983000-158984400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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