Variant report

Variant	rs62400980
Chromosome Location	chr6:30795947-30795948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30795677..30797852-chr6:30845172..30846174,17	K562	blood:
2	chr6:30794974..30797453-chr6:30880816..30883631,3	MCF-7	breast:
3	chr6:30787789..30791714-chr6:30792255..30797305,10	K562	blood:
4	chr6:30735516..30738178-chr6:30794315..30796554,3	MCF-7	breast:
5	chr6:30794499..30796682-chr6:30796946..30799909,4	K562	blood:
6	chr6:30792900..30798152-chr6:30848587..30855236,10	MCF-7	breast:
7	chr6:30786581..30788295-chr6:30794168..30796085,2	MCF-7	breast:
8	chr6:30794216..30799803-chr6:30838849..30846731,16	K562	blood:
9	chr6:30793814..30798702-chr6:30880453..30884092,5	K562	blood:
10	chr6:30787837..30792214-chr6:30792255..30797817,7	K562	blood:
11	chr6:30795223..30797850-chr6:30849493..30851248,2	K562	blood:
12	chr6:30794896..30797869-chr6:30842153..30843762,2	K562	blood:
13	chr6:30795938..30797474-chr6:30860492..30861360,6	K562	blood:
14	chr6:30709015..30713327-chr6:30792572..30798179,6	K562	blood:
15	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
16	chr3:63497233..63499254-chr6:30795355..30797782,2	MCF-7	breast:
17	chr6:30738970..30741977-chr6:30793706..30796488,3	MCF-7	breast:
18	chr6:30792780..30797161-chr6:30880651..30883443,6	K562	blood:
19	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
20	chr6:30794216..30796445-chr6:30839045..30841799,3	K562	blood:
21	chr6:30795918..30796957-chr6:30845184..30846122,7	MCF-7	breast:
22	chr3:64147440..64150145-chr6:30794750..30796376,2	MCF-7	breast:
23	chr6:30794393..30796248-chr6:30844324..30846676,2	K562	blood:
24	chr6:30792427..30796566-chr6:30845190..30846951,4	MCF-7	breast:
25	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
26	chr6:30686162..30687750-chr6:30794446..30796448,2	MCF-7	breast:
27	chr6:30794295..30796763-chr6:31046294..31048518,2	K562	blood:
28	chr6:30733982..30738634-chr6:30792613..30796884,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000201988	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000263608	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10807071	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12189560	0.83[EUR][1000 genomes]
rs12189986	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12190167	0.88[EUR][1000 genomes]
rs12190453	0.85[EUR][1000 genomes]
rs12190527	0.92[AFR][1000 genomes]
rs12192177	0.82[EUR][1000 genomes]
rs12192178	0.82[EUR][1000 genomes]
rs12192205	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12192430	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192704	0.85[EUR][1000 genomes]
rs12192760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192828	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195469	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12195508	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195605	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12195964	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12197154	0.87[EUR][1000 genomes]
rs12197221	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198723	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198842	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12199559	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12199612	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12200562	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12200829	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12202570	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12202778	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12202957	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12203011	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12203199	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12203797	0.85[EUR][1000 genomes]
rs12204146	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12204167	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12205844	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205961	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206022	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12206742	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12206930	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12207652	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12208098	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12208771	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12209725	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12210111	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210318	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210590	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12212837	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213493	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12213497	0.85[EUR][1000 genomes]
rs12214232	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12214398	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12215119	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264372	0.82[ASN][1000 genomes]
rs16897921	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs16897932	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17189483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17189490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195830	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195837	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394414	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28744161	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28744171	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28766294	0.86[EUR][1000 genomes]
rs28830248	0.88[AFR][1000 genomes]
rs28877339	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28890780	0.83[EUR][1000 genomes]
rs4248152	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4327730	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4409219	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711240	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4711241	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4713373	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4713376	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4713386	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4713387	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4713388	0.85[EUR][1000 genomes]
rs4713391	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4995774	0.84[AFR][1000 genomes]
rs59293911	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62400964	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400965	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62400966	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62400977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400978	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400979	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62400981	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62408707	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62408708	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62408709	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62408712	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62408713	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62408715	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62408716	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62408717	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62408723	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62408724	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62408725	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62408726	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62408727	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62408728	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9501488	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription 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 target site	223 gene(s)	inside rSNPs	diseases
7	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
8	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30782000-30796000	Weak transcription	Pancreas	Pancrea
2	chr6:30782000-30797000	Weak transcription	Gastric	stomach
3	chr6:30788400-30796000	Weak transcription	Lung	lung
4	chr6:30790200-30796200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:30790600-30796000	Weak transcription	Fetal Lung	lung
6	chr6:30792400-30796400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:30792600-30796000	Weak transcription	Spleen	Spleen
8	chr6:30793600-30796000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:30794000-30796000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:30794000-30796000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:30794200-30796000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr6:30794200-30796000	Enhancers	K562	blood
13	chr6:30794400-30798400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:30794400-30798400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:30794600-30796000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:30794600-30796000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr6:30794600-30796000	Enhancers	Duodenum Mucosa	Duodenum
18	chr6:30794600-30796000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr6:30794600-30796000	Enhancers	HSMM	muscle
20	chr6:30794600-30796000	Enhancers	NHEK	skin
21	chr6:30794600-30796200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:30794600-30796200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:30794600-30796400	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr6:30794600-30796600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:30794600-30796800	Enhancers	Fetal Intestine Large	intestine
26	chr6:30794600-30796800	Enhancers	Stomach Mucosa	stomach
27	chr6:30794600-30796800	Enhancers	HUVEC	blood vessel
28	chr6:30794600-30796800	Enhancers	NH-A	brain
29	chr6:30794600-30797200	Enhancers	HMEC	breast
30	chr6:30794600-30797400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:30794800-30796000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:30794800-30796000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:30794800-30796000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:30794800-30796000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr6:30794800-30796000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:30794800-30796000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:30794800-30796400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:30794800-30796800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:30794800-30796800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:30794800-30796800	Enhancers	GM12878-XiMat	blood
41	chr6:30794800-30797000	Enhancers	NHLF	lung
42	chr6:30794800-30797200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:30794800-30797200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:30794800-30797200	Enhancers	Colonic Mucosa	Colon
45	chr6:30794800-30797200	Enhancers	Psoas Muscle	Psoas
46	chr6:30794800-30797400	Enhancers	Placenta	Placenta
47	chr6:30794800-30797800	Enhancers	Dnd41	blood
48	chr6:30795000-30796400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr6:30795000-30796600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:30795000-30798800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links