Variant report

Variant	rs62152868
Chromosome Location	chr2:97537070-97537071
allele	C/T
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	MAX	chr2:97535320-97537114	K562	blood:	n/a	chr2:97535876-97535886 chr2:97537007-97537015
2	POLR2A	chr2:97537064-97537181	MCF10A-Er-Src	breast:	n/a	n/a
3	MAFF	chr2:97536410-97537107	K562	blood:	n/a	chr2:97536819-97536837 chr2:97536818-97536832
4	TBL1XR1	chr2:97536326-97537125	K562	blood:	n/a	n/a
5	SIN3AK20	chr2:97531740-97537442	MCF-7	breast:	n/a	n/a
6	POLR2A	chr2:97534104-97537233	K562	blood:	n/a	n/a
7	MAX	chr2:97535508-97537269	K562	blood:	n/a	chr2:97535876-97535886 chr2:97537007-97537015
8	POLR2A	chr2:97531939-97537196	K562	blood:	n/a	n/a
9	MAZ	chr2:97534161-97537108	K562	blood:	n/a	chr2:97535876-97535886 chr2:97537007-97537015 chr2:97534898-97534908
10	MXI1	chr2:97536042-97537108	K562	blood:	n/a	chr2:97536650-97536659
11	JUND	chr2:97536524-97537183	K562	blood:	n/a	n/a
12	POLR2A	chr2:97534163-97537107	K562	blood:	n/a	n/a
13	POLR2A	chr2:97528920-97537556	K562	blood:	n/a	n/a
14	RCOR1	chr2:97535686-97537201	K562	blood:	n/a	n/a
15	MYC	chr2:97534094-97537261	K562	blood:	n/a	chr2:97535876-97535886 chr2:97537007-97537015 chr2:97534898-97534908
16	EP300	chr2:97536402-97537084	K562	blood:	n/a	chr2:97536634-97536650
17	POLR2A	chr2:97536079-97537210	K562	blood:	n/a	n/a
18	GTF2F1	chr2:97536321-97537079	K562	blood:	n/a	n/a
19	GATA2	chr2:97536894-97537245	K562	blood:	n/a	chr2:97537161-97537174
20	HDAC2	chr2:97536303-97537171	MCF-7	breast:	n/a	chr2:97537035-97537049 chr2:97537036-97537050 chr2:97537039-97537053
21	POLR2A	chr2:97533304-97537101	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr2:97535585-97537280	K562	blood:	n/a	n/a
23	TAF1	chr2:97535057-97537273	MCF-7	breast:	n/a	n/a
24	POLR2A	chr2:97528940-97537661	K562	blood:	n/a	n/a
25	RCOR1	chr2:97536648-97537081	K562	blood:	n/a	n/a
26	TCF7L2	chr2:97536288-97537113	Hela-S3	cervix:	n/a	chr2:97536501-97536510
27	SIN3AK20	chr2:97535643-97537202	MCF-7	breast:	n/a	n/a
28	GATA2	chr2:97536876-97537245	SH-SY5Y	brain:	n/a	chr2:97537161-97537174
29	MYC	chr2:97534107-97537114	K562	blood:	n/a	chr2:97535876-97535886 chr2:97537007-97537015 chr2:97534898-97534908
30	MAFK	chr2:97536445-97537193	K562	blood:	n/a	chr2:97536820-97536836 chr2:97536815-97536835 chr2:97536820-97536835 chr2:97536825-97536836

No.	Distal block	Cell Line	Cell type
1	chr2:97481648..97486150-chr2:97531417..97538119,10	MCF-7	breast:
2	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
3	chr2:97534494..97537243-chr9:131936741..131939125,2	MCF-7	breast:
4	chr2:97536575..97540877-chr2:97558007..97561072,4	K562	blood:
5	chr2:97534744..97537184-chr2:97615647..97618608,4	K562	blood:
6	chr2:97506571..97510288-chr2:97534230..97537776,5	MCF-7	breast:
7	chr2:97534211..97537154-chr6:26181504..26183977,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNNM3-3	chr2:97535853-97537289	NONHSAT072592

Variant related genes	Relation type
SEMA4C	TF binding region
ENSG00000163126	Chromatin interaction
ENSG00000168754	Chromatin interaction
ENSG00000204055	Chromatin interaction
ENSG00000268050	Chromatin interaction
ENSG00000197697	Chromatin interaction
ENSG00000252845	Chromatin interaction
ENSG00000168763	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6707255	0.84[AFR][1000 genomes]
rs7597743	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 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	chr2:97533800-97537200	Active TSS	Gastric	stomach
2	chr2:97536000-97537200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:97536000-97537200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:97536000-97537200	Flanking Active TSS	Brain Germinal Matrix	brain
5	chr2:97536200-97537200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
6	chr2:97536200-97537200	Flanking Active TSS	Brain Cingulate Gyrus	brain
7	chr2:97536200-97537200	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr2:97536200-97537200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
9	chr2:97536200-97537200	Flanking Active TSS	Rectal Smooth Muscle	rectum
10	chr2:97536200-97537200	Flanking Active TSS	Hela-S3	cervix
11	chr2:97536200-97537400	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr2:97536400-97537200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr2:97536400-97537400	Enhancers	Fetal Heart	heart
14	chr2:97536400-97538400	Weak transcription	HMEC	breast
15	chr2:97536400-97539800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:97536600-97537200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:97536600-97537200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:97536600-97537200	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:97536600-97537200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:97536600-97537200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr2:97536600-97538400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:97536600-97541600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr2:97536800-97537200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
24	chr2:97536800-97537200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr2:97536800-97537200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr2:97536800-97537200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:97536800-97537200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:97536800-97537200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:97536800-97537200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:97536800-97537200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:97536800-97537200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr2:97536800-97537200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:97536800-97537200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:97536800-97537200	Enhancers	Brain Angular Gyrus	brain
35	chr2:97536800-97537200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:97536800-97537200	Enhancers	Brain Substantia Nigra	brain
37	chr2:97536800-97537200	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr2:97536800-97537200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
39	chr2:97536800-97537200	Enhancers	Esophagus	oesophagus
40	chr2:97536800-97537200	Enhancers	Fetal Brain Female	brain
41	chr2:97536800-97537200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr2:97536800-97537200	Bivalent Enhancer	Fetal Muscle Leg	muscle
43	chr2:97536800-97537200	Enhancers	Pancreas	Pancrea
44	chr2:97536800-97537200	Enhancers	GM12878-XiMat	blood
45	chr2:97536800-97537200	Transcr. at gene 5' and 3'	K562	blood
46	chr2:97536800-97537200	Enhancers	NHDF-Ad	bronchial
47	chr2:97536800-97537200	Enhancers	NHEK	skin
48	chr2:97536800-97537400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:97536800-97537400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr2:97536800-97537400	Enhancers	Lung	lung

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