Variant report

Variant	rs9286893
Chromosome Location	chr1:173829423-173829424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:173829312-173829524	U87	brain:	n/a	n/a
2	POLR2A	chr1:173828332-173838242	K562	blood:	n/a	n/a
3	POLR2A	chr1:173829190-173829554	U87	brain:	n/a	n/a
4	POLR2A	chr1:173828719-173829629	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:173829108-173830485	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr1:173829381-173833686	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:173825088-173838434	K562	blood:	n/a	n/a
8	POLR2A	chr1:173827997-173836225	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:173824570-173837689	A549	lung:	n/a	n/a
10	POLR2A	chr1:173828233-173834504	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:173829284-173838362	K562	blood:	n/a	n/a
12	POLR2A	chr1:173829132-173838052	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr1:173829033-173834330	U87	brain:	n/a	n/a
14	CUX1	chr1:173829323-173829806	K562	blood:	n/a	n/a
15	POLR2A	chr1:173829120-173838093	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:173828322-173838150	H1-hESC	embryonic stem cell:	n/a	n/a
17	HEY1	chr1:173829217-173829479	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:173829165-173838292	GM19099	blood:	n/a	n/a
19	POLR2A	chr1:173829350-173838204	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:173828141-173838409	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr1:173828164-173834063	IMR90	lung:	n/a	n/a
22	POLR2A	chr1:173829248-173838155	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:173828033-173838432	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:173829160-173834503	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:173829145-173838211	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:173828415-173838818	GM12891	blood:	n/a	n/a
27	POLR2A	chr1:173829313-173834335	GM12891	blood:	n/a	n/a
28	POLR2A	chr1:173822006-173838661	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr1:173828493-173834145	HUVEC	blood vessel:	n/a	n/a
30	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
31	POLR2A	chr1:173828900-173838489	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:173828351-173829844	K562	blood:	n/a	n/a
33	POLR2A	chr1:173824562-173838422	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr1:173829116-173838152	GM12892	blood:	n/a	n/a
35	POLR2A	chr1:173825936-173838412	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:173828318-173838414	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:173828726-173834273	U87	brain:	n/a	n/a
38	POLR2A	chr1:173829388-173830286	PBDE	blood:	n/a	n/a
39	POLR2A	chr1:173828186-173838134	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr1:173828328-173834376	K562	blood:	n/a	n/a
41	POLR2A	chr1:173824467-173838308	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:173828381-173830576	HL-60	blood:	n/a	n/a
43	POLR2A	chr1:173828495-173837822	HepG2	liver:	n/a	n/a
44	POLR2A	chr1:173829315-173838297	K562	blood:	n/a	n/a
45	POLR2A	chr1:173828740-173834326	HUVEC	blood vessel:	n/a	n/a
46	CHD2	chr1:173829230-173830217	K562	blood:	n/a	n/a
47	POLR2A	chr1:173828548-173838403	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr1:173829208-173838339	GM12878	blood:	n/a	n/a

No data

(count:13 , 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	chr1:173682439..173685635-chr1:173828531..173832401,4	MCF-7	breast:
12	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:
13	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
ENSG00000117593	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000006194	Chromatin interaction
ENSG00000076321	Chromatin interaction
ENSG00000120334	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10082296	1.00[AMR][1000 genomes]
rs10128064	1.00[AMR][1000 genomes]
rs10158274	1.00[AMR][1000 genomes]
rs10159349	1.00[AMR][1000 genomes]
rs12239406	1.00[AMR][1000 genomes]
rs13313018	1.00[AMR][1000 genomes]
rs13374735	1.00[AMR][1000 genomes]
rs13375569	1.00[AMR][1000 genomes]
rs13376339	1.00[AMR][1000 genomes]
rs2227605	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2227621	1.00[AMR][1000 genomes]
rs4650988	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4652416	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6425252	1.00[AMR][1000 genomes]
rs6656810	1.00[AMR][1000 genomes]
rs6665497	1.00[AMR][1000 genomes]
rs7349122	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7349166	0.81[AFR][1000 genomes]
rs9425412	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425417	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425429	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425432	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425437	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425732	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425733	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425737	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425739	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425743	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425744	1.00[AMR][1000 genomes]
rs9425767	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425769	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425770	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425771	0.81[AFR][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	chr1:173813200-173831800	Weak transcription	Right Ventricle	heart
10	chr1:173813200-173832000	Weak transcription	Small Intestine	intestine
11	chr1:173813400-173831000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:173818200-173831600	Weak transcription	Fetal Brain Male	brain
13	chr1:173818400-173829800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:173818600-173829600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:173818600-173830200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr1:173818600-173834800	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:173818600-173834800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:173819200-173833200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:173819200-173833800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:173819200-173834000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:173819400-173829800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:173819400-173832000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:173819400-173834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:173819600-173830000	Weak transcription	Right Atrium	heart
25	chr1:173819600-173834000	Strong transcription	Fetal Thymus	thymus
26	chr1:173819600-173835600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:173820600-173833800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:173820600-173834000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:173821000-173834000	Strong transcription	Liver	Liver
30	chr1:173821000-173834000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr1:173822000-173834000	Strong transcription	Fetal Intestine Large	intestine
32	chr1:173822400-173832600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:173822400-173833600	Strong transcription	Fetal Brain Female	brain
34	chr1:173822400-173833800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:173822800-173829600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:173822800-173830800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:173822800-173831000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:173822800-173831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:173822800-173832400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:173822800-173832400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:173822800-173833400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:173822800-173834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:173823000-173829600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:173823000-173831600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:173823000-173831800	Weak transcription	NHLF	lung
46	chr1:173823000-173835000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr1:173823200-173830200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:173823200-173833400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:173823400-173831400	Weak transcription	Pancreas	Pancrea
50	chr1:173823400-173832200	Weak transcription	Rectal Smooth Muscle	rectum

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