Variant report

Variant	rs2517578
Chromosome Location	chr6:30811265-30811266
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30709488..30712315-chr6:30811079..30813946,2	MCF-7	breast:
2	chr6:30811247..30813730-chr6:30844224..30845960,2	K562	blood:
3	chr6:30710179..30712517-chr6:30808321..30811657,4	MCF-7	breast:
4	chr6:30708712..30711147-chr6:30810186..30812455,3	K562	blood:
5	chr6:30810334..30813136-chr6:30813626..30816587,2	K562	blood:
6	chr6:30796462..30798109-chr6:30809712..30812488,2	K562	blood:
7	chr6:30809749..30812115-chr6:30849210..30852847,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-12	chr6:30811155-30812133	NONHSAT108684

No data

Variant related genes	Relation type
ENSG00000137331	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000237923	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1049633	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1059612	0.90[AMR][1000 genomes]
rs11755837	1.00[ASN][1000 genomes]
rs1264308	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264325	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264351	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1264361	0.87[EUR][1000 genomes]
rs1264373	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1634716	1.00[AMR][1000 genomes]
rs1634721	1.00[AMR][1000 genomes]
rs1634726	0.89[AMR][1000 genomes]
rs2263298	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2524266	0.92[EUR][1000 genomes]
rs2535328	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535340	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2844656	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2844661	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28674977	1.00[ASN][1000 genomes]
rs3094088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095152	0.81[AMR][1000 genomes]
rs3095153	0.81[AMR][1000 genomes]
rs3095156	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3095326	0.81[AMR][1000 genomes]
rs3095328	0.81[AMR][1000 genomes]
rs3095332	0.81[AMR][1000 genomes]
rs3129973	0.81[AMR][1000 genomes]
rs3129974	0.81[AMR][1000 genomes]
rs3129980	0.80[EUR][1000 genomes]
rs3129982	0.80[EUR][1000 genomes]
rs3129983	0.80[EUR][1000 genomes]
rs3129984	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129985	0.80[EUR][1000 genomes]
rs3130641	0.83[EUR][1000 genomes]
rs3130668	0.81[AMR][1000 genomes]
rs3131041	0.82[EUR][1000 genomes]
rs3131044	0.80[EUR][1000 genomes]
rs3131045	0.80[EUR][1000 genomes]
rs3131047	0.80[EUR][1000 genomes]
rs3131049	0.80[EUR][1000 genomes]
rs3131050	0.80[EUR][1000 genomes]
rs3131052	0.81[EUR][1000 genomes]
rs3131055	0.80[EUR][1000 genomes]
rs3131058	0.80[EUR][1000 genomes]
rs3131060	0.80[EUR][1000 genomes]
rs3131781	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3132577	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132580	0.81[AMR][1000 genomes]
rs3132581	0.81[AMR][1000 genomes]
rs3132600	0.81[EUR][1000 genomes]
rs886422	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs886424	0.87[EUR][1000 genomes]
rs886425	0.87[EUR][1000 genomes]
rs9262141	0.90[AMR][1000 genomes]
rs9262142	0.90[AMR][1000 genomes]
rs9262146	0.90[AMR][1000 genomes]
rs9262200	0.80[EUR][1000 genomes]
rs9262202	0.80[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2517578	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30797200-30812000	Weak transcription	Lung	lung
2	chr6:30799200-30812200	Weak transcription	Spleen	Spleen
3	chr6:30803200-30811400	Enhancers	Fetal Thymus	thymus
4	chr6:30803200-30811400	Enhancers	Thymus	Thymus
5	chr6:30804600-30811600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:30806600-30811600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:30806800-30811400	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr6:30806800-30816200	Enhancers	Placenta	Placenta
9	chr6:30807400-30812200	Enhancers	Duodenum Mucosa	Duodenum
10	chr6:30807800-30811400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:30807800-30811400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:30808200-30812000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:30808200-30813600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:30808600-30811600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:30809000-30811800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:30809400-30811600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr6:30809600-30811800	Weak transcription	Esophagus	oesophagus
18	chr6:30809800-30811400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:30810000-30813400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:30810200-30811400	Weak transcription	Hela-S3	cervix
21	chr6:30810200-30811400	Weak transcription	HMEC	breast
22	chr6:30810200-30811600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:30810200-30811600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:30810200-30811600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:30810200-30811600	Weak transcription	Stomach Mucosa	stomach
26	chr6:30810600-30811400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:30810600-30811800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr6:30810800-30811600	Enhancers	HSMMtube	muscle
29	chr6:30810800-30811800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:30810800-30812000	Enhancers	Osteobl	bone
31	chr6:30810800-30812400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:30810800-30812600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:30810800-30812600	Enhancers	Fetal Lung	lung
34	chr6:30810800-30812800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr6:30810800-30813400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:30810800-30814000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:30811000-30811600	Enhancers	NHEK	skin
38	chr6:30811000-30811800	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr6:30811000-30811800	Enhancers	Fetal Stomach	stomach
40	chr6:30811000-30811800	Enhancers	Small Intestine	intestine
41	chr6:30811000-30812000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr6:30811000-30812200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:30811000-30812200	Enhancers	Aorta	Aorta
44	chr6:30811000-30812200	Enhancers	Fetal Intestine Large	intestine
45	chr6:30811000-30812200	Enhancers	Right Ventricle	heart
46	chr6:30811000-30812400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr6:30811000-30812400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr6:30811000-30812400	Enhancers	Fetal Muscle Trunk	muscle
49	chr6:30811000-30812400	Enhancers	Fetal Muscle Leg	muscle
50	chr6:30811000-30812600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links