Variant report

Variant	rs28362370
Chromosome Location	chr2:10590197-10590198
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	YY1	chr2:10590042-10590631	HepG2	liver:	n/a	n/a
2	CEBPD	chr2:10590144-10590459	HepG2	liver:	n/a	chr2:10590269-10590280
3	HEY1	chr2:10589655-10590524	HepG2	liver:	n/a	n/a
4	JUND	chr2:10590087-10590457	Hela-S3	cervix:	n/a	n/a
5	GABPA	chr2:10590128-10590473	HepG2	liver:	n/a	n/a
6	GABPA	chr2:10590138-10590440	HepG2	liver:	n/a	n/a
7	MAX	chr2:10590118-10590618	HepG2	liver:	n/a	n/a
8	ELK1	chr2:10590071-10590444	Hela-S3	cervix:	n/a	chr2:10590291-10590300 chr2:10590291-10590300
9	GABPA	chr2:10590159-10590495	K562	blood:	n/a	n/a
10	CEBPB	chr2:10590166-10590844	H1-hESC	embryonic stem cell:	n/a	chr2:10590269-10590280 chr2:10590268-10590281
11	TCF7L2	chr2:10590030-10590498	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr2:10590040-10590453	Hela-S3	cervix:	n/a	n/a
13	MAFF	chr2:10589875-10590432	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:10587578-10590208	K562	blood:	n/a	n/a
15	GABPA	chr2:10590010-10590637	A549	lung:	n/a	n/a
16	TBP	chr2:10588323-10590473	Hela-S3	cervix:	n/a	n/a
17	USF1	chr2:10590138-10590440	A549	lung:	n/a	n/a
18	CEBPB	chr2:10590028-10590897	HepG2	liver:	n/a	chr2:10590269-10590280 chr2:10590268-10590281
19	CEBPB	chr2:10590079-10590371	ECC-1	luminal epithelium:	n/a	chr2:10590269-10590280 chr2:10590268-10590281
20	HNF4G	chr2:10589891-10590513	HepG2	liver:	n/a	chr2:10590230-10590245 chr2:10590229-10590244 chr2:10590229-10590244
21	HCFC1	chr2:10587990-10590789	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr2:10590111-10590412	HepG2	liver:	n/a	chr2:10590269-10590280 chr2:10590268-10590281
23	RAD21	chr2:10590130-10590428	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr2:10589744-10590589	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr2:10587674-10590729	HepG2	liver:	n/a	n/a
26	MAFK	chr2:10590191-10590429	HepG2	liver:	n/a	n/a
27	POLR2A	chr2:10588710-10590566	HCT-116	colon:	n/a	n/a
28	ELF1	chr2:10590062-10590482	A549	lung:	n/a	chr2:10590287-10590300 chr2:10590289-10590300 chr2:10590289-10590300
29	CEBPB	chr2:10590106-10590449	K562	blood:	n/a	chr2:10590269-10590280 chr2:10590268-10590281
30	MYC	chr2:10590139-10590908	MCF10A-Er-Src	breast:	n/a	n/a
31	BRCA1	chr2:10590159-10590409	HepG2	liver:	n/a	n/a
32	FOSL2	chr2:10589981-10590874	HepG2	liver:	n/a	chr2:10590692-10590706
33	CREB1	chr2:10590049-10590499	A549	lung:	n/a	n/a
34	RFX5	chr2:10589947-10590499	Hela-S3	cervix:	n/a	n/a
35	MYBL2	chr2:10589841-10590647	HepG2	liver:	n/a	n/a
36	MYC	chr2:10589945-10590892	MCF10A-Er-Src	breast:	n/a	n/a
37	CEBPD	chr2:10589897-10590484	HepG2	liver:	n/a	chr2:10590269-10590280
38	POLR2A	chr2:10588692-10590735	HepG2	liver:	n/a	n/a
39	HCFC1	chr2:10590186-10590343	K562	blood:	n/a	n/a
40	POLR2A	chr2:10586448-10590304	IMR90	lung:	n/a	n/a
41	POLR2A	chr2:10589900-10590578	HepG2	liver:	n/a	n/a
42	MXI1	chr2:10589870-10590741	HepG2	liver:	n/a	n/a
43	SMC3	chr2:10590083-10590501	HepG2	liver:	n/a	n/a
44	TAF1	chr2:10590018-10590591	HepG2	liver:	n/a	n/a
45	POLR2A	chr2:10587476-10590717	Raji	blood:	n/a	n/a
46	RCOR1	chr2:10590027-10590520	Hela-S3	cervix:	n/a	n/a
47	NR3C1	chr2:10590105-10590518	A549	lung:	n/a	chr2:10590106-10590119
48	MAX	chr2:10587487-10590646	HCT-116	colon:	n/a	chr2:10588126-10588135 chr2:10588941-10588950 chr2:10588939-10588948 chr2:10588651-10588660 chr2:10588126-10588136 chr2:10588125-10588136 chr2:10588939-10588949 chr2:10588496-10588505 chr2:10588124-10588137 chr2:10588938-10588949 chr2:10589691-10589701 chr2:10588125-10588134 chr2:10588938-10588948 chr2:10588125-10588136 chr2:10588938-10588949 chr2:10588930-10588946 chr2:10588939-10588948 chr2:10588500-10588509 chr2:10588125-10588136 chr2:10588124-10588137 chr2:10588939-10588948
49	MAFK	chr2:10589909-10590815	HepG2	liver:	n/a	chr2:10590016-10590031
50	POLR2A	chr2:10589621-10590561	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10394552..10396984-chr2:10589964..10592378,2	K562	blood:
2	chr2:10259653..10265917-chr2:10585320..10590295,8	MCF-7	breast:
3	chr2:10183697..10185477-chr2:10588092..10590281,2	K562	blood:
4	chr2:10259710..10265084-chr2:10586364..10590442,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPCAL1-1	chr2:10590179-10590407	ENSG00000257135
2	lnc-HPCAL1-1	chr2:10589731-10590781	XLOC_001342
3	lnc-HPCAL1-1	chr2:10589870-10590407	XLOC_001342
4	lnc-HPCAL1-1	chr2:10589581-10590407	XLOC_001342
5	lnc-HPCAL1-1	chr2:10590179-10590407	XLOC_001342
6	lnc-HPCAL1-1	chr2:10588861-10590831	NONHSAT069104
7	lnc-HPCAL1-1	chr2:10590179-10590407	NONHSAT069111
8	lnc-HPCAL1-1	chr2:10589333-10590809	NONHSAT069109

Variant related genes	Relation type
SNORA80B	TF binding region
ODC1	TF binding region
ENSG00000217258	TF binding region
ENSG00000171848	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000172059	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs28362389	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28362391	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28362392	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28362395	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28362400	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28362424	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28362425	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28362430	1.00[AMR][1000 genomes]
rs28362431	1.00[AMR][1000 genomes]
rs56853887	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873646	chr2:10550517-10612091	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv873647	chr2:10576424-10597858	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	nsv873648	chr2:10584639-10599493	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
7	esv1819730	chr2:10585164-10591407	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv1818042	chr2:10585364-10591407	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	esv1840643	chr2:10585364-10607465	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
10	nsv873649	chr2:10585458-10591628	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv873650	chr2:10585458-10597858	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
12	nsv873651	chr2:10585575-10597858	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
13	esv1835530	chr2:10585687-10591407	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	esv1818199	chr2:10587504-10591407	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
15	esv1836092	chr2:10587869-10591407	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
16	esv1835846	chr2:10587869-10591628	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
17	esv1835907	chr2:10587869-10591628	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
18	esv1838652	chr2:10587869-10591628	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
19	esv1844482	chr2:10587869-10591628	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
20	esv1844642	chr2:10587869-10591628	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
21	esv1839493	chr2:10587869-10595578	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
22	esv1841500	chr2:10587869-10595578	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
23	esv1842177	chr2:10587869-10595578	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
24	esv1835263	chr2:10587869-10611211	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10587800-10590200	Active TSS	Rectal Smooth Muscle	rectum
2	chr2:10587800-10590400	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr2:10588800-10590400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:10589000-10590200	Flanking Active TSS	GM12878-XiMat	blood
5	chr2:10589000-10590600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr2:10589000-10591000	Flanking Active TSS	Hela-S3	cervix
7	chr2:10589200-10590200	Flanking Active TSS	Fetal Intestine Small	intestine
8	chr2:10589200-10590200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:10589200-10590400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:10589200-10590400	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr2:10589200-10590600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:10589200-10590800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr2:10589200-10592000	Weak transcription	Gastric	stomach
14	chr2:10589400-10590200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:10589400-10590200	Enhancers	Fetal Brain Male	brain
16	chr2:10589400-10590400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:10589400-10590600	Weak transcription	Ovary	ovary
18	chr2:10589400-10590800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr2:10589400-10592400	Weak transcription	Esophagus	oesophagus
20	chr2:10589600-10590200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:10589600-10590200	Enhancers	Primary hematopoietic stem cells	blood
22	chr2:10589600-10590200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr2:10589600-10590200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:10589600-10590200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:10589600-10590200	Enhancers	NH-A	brain
26	chr2:10589600-10590400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:10589600-10590400	Enhancers	Primary B cells from peripheral blood	blood
28	chr2:10589600-10590400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:10589600-10590400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:10589600-10590400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr2:10589600-10590400	Enhancers	Fetal Muscle Leg	muscle
32	chr2:10589600-10590400	Enhancers	Fetal Stomach	stomach
33	chr2:10589600-10590400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr2:10589600-10590600	Enhancers	Adipose Nuclei	Adipose
35	chr2:10589600-10590600	Enhancers	Colonic Mucosa	Colon
36	chr2:10589600-10590600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:10589600-10590600	Enhancers	HUVEC	blood vessel
38	chr2:10589600-10590800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:10589600-10590800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:10589600-10590800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr2:10589600-10590800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr2:10589600-10590800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr2:10589600-10590800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:10589600-10590800	Bivalent Enhancer	Placenta	Placenta
45	chr2:10589600-10590800	Enhancers	Pancreas	Pancrea
46	chr2:10589600-10591200	Weak transcription	NHLF	lung
47	chr2:10589600-10592000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:10589600-10592000	Weak transcription	Small Intestine	intestine
49	chr2:10589600-10592000	Weak transcription	NHDF-Ad	bronchial
50	chr2:10589600-10592200	Weak transcription	HSMM	muscle

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