Variant report

Variant	rs58688107
Chromosome Location	chr1:149909818-149909819
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	chr1:149908354-149910263	PANC-1	pancreas:	n/a	n/a
2	GATA3	chr1:149908095-149909856	MCF-7	breast:	n/a	chr1:149908929-149908939
3	FOS	chr1:149909194-149910082	MCF10A-Er-Src	breast:	n/a	n/a
4	SMC3	chr1:149908574-149909849	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:149907903-149909997	A549	lung:	n/a	n/a
6	FOXM1	chr1:149909622-149909947	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:149908993-149909956	Hela-S3	cervix:	n/a	n/a
8	TBL1XR1	chr1:149909773-149909940	GM12878	blood:	n/a	n/a
9	KAP1	chr1:149909154-149909891	U2OS	brain:	n/a	n/a
10	RUNX3	chr1:149909649-149909961	GM12878	blood:	n/a	n/a
11	FOS	chr1:149909214-149909914	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr1:149908380-149910074	SK-N-SH	brain:	n/a	n/a
13	MAZ	chr1:149909309-149909888	K562	blood:	n/a	n/a
14	STAT3	chr1:149909120-149909880	MCF10A-Er-Src	breast:	n/a	chr1:149909479-149909488 chr1:149909835-149909846 chr1:149909865-149909872
15	STAT3	chr1:149909137-149909830	MCF10A-Er-Src	breast:	n/a	chr1:149909479-149909488
16	MAZ	chr1:149909701-149909878	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:149908510-149910216	MCF-7	breast:	n/a	n/a
18	MAX	chr1:149908037-149910147	A549	lung:	n/a	n/a
19	POLR2A	chr1:149908514-149910202	HCT-116	colon:	n/a	n/a
20	FOSL2	chr1:149908107-149910069	MCF-7	breast:	n/a	chr1:149909136-149909145
21	TCF12	chr1:149909041-149910032	A549	lung:	n/a	chr1:149909987-149909997
22	IRF1	chr1:149909708-149910007	K562	blood:	n/a	chr1:149909835-149909846 chr1:149909834-149909854 chr1:149909835-149909848 chr1:149909832-149909846 chr1:149909835-149909849 chr1:149909835-149909847 chr1:149909835-149909848 chr1:149909836-149909846 chr1:149909832-149909849 chr1:149909830-149909847 chr1:149909836-149909850 chr1:149909835-149909848
23	SIN3AK20	chr1:149908093-149910331	MCF-7	breast:	n/a	n/a
24	CHD2	chr1:149909750-149909909	GM12878	blood:	n/a	chr1:149909801-149909811
25	BCL3	chr1:149908455-149909869	A549	lung:	n/a	chr1:149909837-149909846 chr1:149909479-149909488 chr1:149909138-149909147
26	RUNX3	chr1:149909609-149909872	GM12878	blood:	n/a	n/a
27	FOSL2	chr1:149908527-149909837	A549	lung:	n/a	chr1:149909136-149909145
28	POLR2A	chr1:149908465-149910129	PANC-1	pancreas:	n/a	n/a
29	SP1	chr1:149908320-149910145	HCT-116	colon:	n/a	chr1:149909801-149909810 chr1:149909075-149909084 chr1:149908772-149908786 chr1:149909076-149909085 chr1:149909076-149909085
30	CHD2	chr1:149909276-149909904	Hela-S3	cervix:	n/a	chr1:149909801-149909811
31	MAX	chr1:149909766-149910002	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:149909572..149911574-chr12:77169108..77170909,2	MCF-7	breast:
2	chr1:149908142..149911040-chr12:120728491..120730750,2	MCF-7	breast:
3	chr1:149815719..149822339-chr1:149907112..149913890,13	MCF-7	breast:
4	chr1:149908788..149910913-chr1:150337065..150338725,2	MCF-7	breast:
5	chr1:149908339..149915829-chr1:150035449..150039990,12	MCF-7	breast:
6	chr1:149908135..149909905-chr13:113655760..113657379,2	MCF-7	breast:
7	chr1:149909021..149910890-chr1:150157727..150159306,2	MCF-7	breast:
8	chr1:149813703..149815713-chr1:149909589..149912575,2	MCF-7	breast:
9	chr1:149909098..149913476-chr1:149978280..149982825,6	MCF-7	breast:
10	chr1:149909612..149912880-chr1:149960948..149964772,4	MCF-7	breast:
11	chr1:149908936..149911322-chr4:84348157..84349658,2	MCF-7	breast:
12	chr1:149908458..149914088-chr1:149980717..149984285,8	MCF-7	breast:
13	chr1:149907171..149915966-chr1:150036158..150043011,15	MCF-7	breast:
14	chr1:149909114..149911303-chr1:149929784..149931394,2	MCF-7	breast:
15	chr1:149908929..149910844-chr1:149992123..149994012,2	MCF-7	breast:
16	chr1:149814002..149823234-chr1:149906555..149912579,18	MCF-7	breast:
17	chr1:149907919..149910778-chr8:101963052..101964882,2	MCF-7	breast:
18	chr1:149909348..149911287-chr1:150133137..150136062,3	MCF-7	breast:
19	chr1:149907301..149909862-chr1:160001168..160003843,2	MCF-7	breast:
20	chr1:149909776..149912433-chr1:150001738..150003437,2	MCF-7	breast:
21	chr1:149909521..149911274-chr3:64794861..64796747,2	MCF-7	breast:

Variant related genes	Relation type
MTMR11	TF binding region
ENSG00000163312	Chromatin interaction
ENSG00000272993	Chromatin interaction
ENSG00000203819	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000203812	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000183558	Chromatin interaction
ENSG00000143315	Chromatin interaction
ENSG00000261716	Chromatin interaction
ENSG00000126217	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000220323	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1556934	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs15916	0.83[AMR][1000 genomes]
rs16832989	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16832993	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833048	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16836857	1.00[AMR][1000 genomes]
rs16837054	1.00[AMR][1000 genomes]
rs16837367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16837593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16838449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16838646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841141	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841623	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841697	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56929499	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57020352	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57182882	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57513077	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58100431	1.00[AMR][1000 genomes]
rs58137104	0.83[AMR][1000 genomes]
rs58777569	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59462540	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59709800	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59934949	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60631776	1.00[AMR][1000 genomes]
rs6664973	1.00[AMR][1000 genomes]
rs6680574	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6694482	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6700399	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73004328	1.00[AMR][1000 genomes]
rs73004398	1.00[AMR][1000 genomes]
rs73004400	1.00[AMR][1000 genomes]
rs73006303	1.00[AMR][1000 genomes]
rs73006306	1.00[AMR][1000 genomes]
rs73006313	1.00[AMR][1000 genomes]
rs73006316	1.00[AMR][1000 genomes]
rs73006318	1.00[AMR][1000 genomes]
rs73006327	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73006333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008191	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008199	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008201	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010104	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010113	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010183	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010186	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010189	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011904	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011906	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011909	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011910	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011912	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011913	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011915	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011930	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73016112	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7523560	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7543861	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432820	chr1:148921404-149920927	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	784 gene(s)	inside rSNPs	diseases
2	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149906400-149912000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:149907800-149910000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr1:149907800-149910000	Flanking Active TSS	Hela-S3	cervix
4	chr1:149908600-149910000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr1:149908600-149911600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
6	chr1:149908800-149910000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:149908800-149910000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:149908800-149910000	Enhancers	Primary T cells from cord blood	blood
9	chr1:149908800-149910000	Enhancers	Lung	lung
10	chr1:149908800-149910000	Enhancers	Small Intestine	intestine
11	chr1:149908800-149910000	Flanking Active TSS	NHLF	lung
12	chr1:149908800-149910200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:149908800-149910200	Enhancers	Liver	Liver
14	chr1:149908800-149910200	Enhancers	Spleen	Spleen
15	chr1:149908800-149910800	Enhancers	Pancreas	Pancrea
16	chr1:149908800-149911000	Enhancers	Psoas Muscle	Psoas
17	chr1:149908800-149911400	Enhancers	Fetal Thymus	thymus
18	chr1:149908800-149912600	Weak transcription	Gastric	stomach
19	chr1:149909000-149910000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:149909000-149910000	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:149909000-149910200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:149909000-149910200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:149909000-149910200	Enhancers	HSMM	muscle
24	chr1:149909000-149910200	Enhancers	HSMMtube	muscle
25	chr1:149909000-149910600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:149909000-149910600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr1:149909000-149910800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:149909000-149910800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:149909000-149911400	Enhancers	Right Ventricle	heart
30	chr1:149909000-149911600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr1:149909000-149911800	Enhancers	Left Ventricle	heart
32	chr1:149909000-149912000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:149909000-149912000	Enhancers	Brain Angular Gyrus	brain
34	chr1:149909200-149910000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:149909200-149910000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr1:149909200-149910000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:149909200-149910000	Flanking Active TSS	Colonic Mucosa	Colon
38	chr1:149909200-149910000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:149909200-149910000	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr1:149909200-149910200	Enhancers	Brain Hippocampus Middle	brain
41	chr1:149909200-149910200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:149909200-149910200	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr1:149909200-149910200	Enhancers	Esophagus	oesophagus
44	chr1:149909200-149910200	Enhancers	Fetal Heart	heart
45	chr1:149909200-149910400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:149909200-149910400	Enhancers	Ovary	ovary
47	chr1:149909200-149910400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr1:149909200-149910800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:149909200-149910800	Enhancers	Placenta	Placenta
50	chr1:149909200-149910800	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links