Variant report

Variant	rs12138407
Chromosome Location	chr1:173829180-173829181
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:173828332-173838242	K562	blood:	n/a	n/a
2	POLR2A	chr1:173828719-173829629	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:173829108-173830485	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:173825088-173838434	K562	blood:	n/a	n/a
5	POLR2A	chr1:173827997-173836225	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:173824570-173837689	A549	lung:	n/a	n/a
7	POLR2A	chr1:173828233-173834504	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:173829132-173838052	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr1:173828729-173829231	MCF-7	breast:	n/a	n/a
10	POLR2A	chr1:173829033-173834330	U87	brain:	n/a	n/a
11	POLR2A	chr1:173829120-173838093	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:173828322-173838150	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:173829165-173838292	GM19099	blood:	n/a	n/a
14	POLR2A	chr1:173828324-173829200	K562	blood:	n/a	n/a
15	POLR2A	chr1:173828141-173838409	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr1:173828164-173834063	IMR90	lung:	n/a	n/a
17	POLR2A	chr1:173828033-173838432	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:173829160-173834503	GM12892	blood:	n/a	n/a
19	POLR2A	chr1:173829145-173838211	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr1:173828415-173838818	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:173822006-173838661	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr1:173828493-173834145	HUVEC	blood vessel:	n/a	n/a
23	BCL3	chr1:173828332-173837889	A549	lung:	n/a	chr1:173837867-173837876 chr1:173837620-173837629 chr1:173831994-173832003 chr1:173837837-173837850 chr1:173837840-173837849 chr1:173837834-173837847
24	POLR2A	chr1:173828900-173838489	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:173828351-173829844	K562	blood:	n/a	n/a
26	POLR2A	chr1:173824562-173838422	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr1:173829116-173838152	GM12892	blood:	n/a	n/a
28	POLR2A	chr1:173825936-173838412	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr1:173828318-173838414	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:173828726-173834273	U87	brain:	n/a	n/a
31	POLR2A	chr1:173828295-173829190	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr1:173828186-173838134	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr1:173828328-173834376	K562	blood:	n/a	n/a
34	POLR2A	chr1:173824467-173838308	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:173828381-173830576	HL-60	blood:	n/a	n/a
36	POLR2A	chr1:173828495-173837822	HepG2	liver:	n/a	n/a
37	POLR2A	chr1:173828740-173834326	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr1:173828548-173838403	HUVEC	blood vessel:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173828069..173829648-chr1:173869495..173872010,2	K562	blood:
2	chr1:173828497..173830034-chr16:3313328..3315238,2	K562	blood:
3	chr1:173829121..173831364-chr1:173963945..173965806,2	MCF-7	breast:
4	chr1:173400530..173402546-chr1:173829006..173830851,2	K562	blood:
5	chr1:173828767..173831620-chr1:173909948..173912434,2	K562	blood:
6	chr1:173828135..173830893-chr1:173854579..173857617,3	MCF-7	breast:
7	chr1:173642158..173644054-chr1:173829177..173831512,2	K562	blood:
8	chr1:173789792..173811494-chr1:173827886..173840273,103	K562	blood:
9	chr1:173826504..173829648-chr1:173870510..173874111,3	K562	blood:
10	chr1:173397788..173400403-chr1:173827176..173829945,2	K562	blood:
11	chr1:173827518..173829337-chr1:174042561..174045221,2	MCF-7	breast:
12	chr1:173682439..173685635-chr1:173828531..173832401,4	MCF-7	breast:
13	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:
14	chr1:173826383..173830416-chr1:173877536..173882048,5	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SERPINC1-1	chr1:173827684-173834420	NONHSAT007659

No data

Variant related genes	Relation type
GAS5-AS1	TF binding region
ENSG00000076321	Chromatin interaction
ENSG00000006194	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000117593	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12117115	1.00[ASN][1000 genomes]
rs12137553	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746886	0.93[AMR][1000 genomes]
rs12749768	1.00[ASN][1000 genomes]
rs34997480	1.00[ASN][1000 genomes]
rs35872531	1.00[ASN][1000 genomes]
rs55762016	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
6	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:173809800-173831800	Weak transcription	Colonic Mucosa	Colon
9	chr1:173811200-173829200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:173813200-173831800	Weak transcription	Right Ventricle	heart
11	chr1:173813200-173832000	Weak transcription	Small Intestine	intestine
12	chr1:173813400-173831000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:173818200-173831600	Weak transcription	Fetal Brain Male	brain
14	chr1:173818400-173829800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:173818600-173829600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:173818600-173830200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:173818600-173834800	Strong transcription	Fetal Muscle Leg	muscle
18	chr1:173818600-173834800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:173819200-173833200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:173819200-173833800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:173819200-173834000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:173819400-173829800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:173819400-173832000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:173819400-173834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:173819600-173830000	Weak transcription	Right Atrium	heart
26	chr1:173819600-173834000	Strong transcription	Fetal Thymus	thymus
27	chr1:173819600-173835600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr1:173820600-173833800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:173820600-173834000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr1:173821000-173834000	Strong transcription	Liver	Liver
31	chr1:173821000-173834000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr1:173821800-173829400	Strong transcription	Placenta	Placenta
33	chr1:173822000-173834000	Strong transcription	Fetal Intestine Large	intestine
34	chr1:173822400-173832600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:173822400-173833600	Strong transcription	Fetal Brain Female	brain
36	chr1:173822400-173833800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:173822800-173829600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:173822800-173830800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:173822800-173831000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:173822800-173831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:173822800-173832400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:173822800-173832400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:173822800-173833400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:173822800-173834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:173823000-173829600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:173823000-173831600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:173823000-173831800	Weak transcription	NHLF	lung
48	chr1:173823000-173835000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr1:173823200-173830200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:173823200-173833400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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