Variant report

Variant	rs1264352
Chromosome Location	chr6:30789647-30789648
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:29)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30687583..30690453-chr6:30788279..30790519,3	MCF-7	breast:
2	chr6:30788846..30792943-chr6:30842643..30845954,4	K562	blood:
3	chr6:30788219..30790360-chr6:31110500..31112207,2	MCF-7	breast:
4	chr6:30786994..30789878-chr6:30922347..30924332,2	K562	blood:
5	chr6:30715944..30717540-chr6:30787940..30790254,2	K562	blood:
6	chr6:30690499..30693062-chr6:30788565..30790679,2	MCF-7	breast:
7	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
8	chr6:30782149..30783848-chr6:30788583..30790085,2	MCF-7	breast:
9	chr6:30784917..30788265-chr6:30788350..30790459,3	K562	blood:
10	chr6:30789462..30790321-chr6:30882992..30883906,2	K562	blood:
11	chr6:30735402..30739247-chr6:30785239..30791444,10	MCF-7	breast:
12	chr6:30789581..30790517-chr6:31055362..31055927,3	K562	blood:
13	chr6:30785152..30790346-chr6:30842867..30847278,6	K562	blood:
14	chr6:30788098..30790149-chr6:30839123..30842076,2	K562	blood:
15	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
16	chr6:30710229..30713248-chr6:30788195..30791151,4	K562	blood:
17	chr6:30694636..30696358-chr6:30788592..30791356,2	K562	blood:
18	chr6:30710040..30710740-chr6:30789594..30790207,2	MCF-7	breast:
19	chr6:30787837..30792214-chr6:30792255..30797817,7	K562	blood:
20	chr6:30709253..30713765-chr6:30784905..30790853,10	K562	blood:
21	chr6:30775890..30781762-chr6:30785090..30789723,9	MCF-7	breast:
22	chr6:30789442..30790123-chr6:30845044..30846033,2	MCF-7	breast:
23	chr6:30762133..30768787-chr6:30785989..30790050,8	MCF-7	breast:
24	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
25	chr6:30723362..30725478-chr6:30789187..30791435,2	MCF-7	breast:
26	chr6:30784327..30791562-chr6:30848580..30853873,26	MCF-7	breast:
27	chr6:30789508..30790311-chr6:31051825..31052620,2	K562	blood:
28	chr6:30787789..30791714-chr6:30792255..30797305,10	K562	blood:
29	chr6:30779954..30784896-chr6:30785156..30789787,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DDR1-4	chr6:30789405-30790045	NONHSAT108683

No data

Variant related genes	Relation type
ENSG00000204580	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000201988	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000233529	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1049943	0.83[ASN][1000 genomes]
rs1061397	0.83[ASN][1000 genomes]
rs10947088	0.83[ASN][1000 genomes]
rs10947089	0.83[ASN][1000 genomes]
rs1136719	0.83[ASN][1000 genomes]
rs11757629	0.91[ASN][1000 genomes]
rs12111310	0.85[ASN][1000 genomes]
rs15297	0.83[ASN][1000 genomes]
rs17195712	0.83[ASN][1000 genomes]
rs17719	0.83[ASN][1000 genomes]
rs28600807	0.83[ASN][1000 genomes]
rs2894045	0.91[ASN][1000 genomes]
rs3094128	0.80[ASN][1000 genomes]
rs3129986	0.97[ASN][1000 genomes]
rs3130662	0.83[ASN][1000 genomes]
rs3131062	0.97[ASN][1000 genomes]
rs3131064	0.97[ASN][1000 genomes]
rs3909184	0.83[ASN][1000 genomes]
rs41270529	0.83[ASN][1000 genomes]
rs58638768	0.83[ASN][1000 genomes]
rs6926530	0.91[ASN][1000 genomes]
rs9262207	0.94[ASN][1000 genomes]
rs9262211	0.94[ASN][1000 genomes]
rs9262215	0.94[ASN][1000 genomes]
rs9262216	0.94[ASN][1000 genomes]
rs9262217	0.94[ASN][1000 genomes]
rs9262218	0.94[ASN][1000 genomes]
rs9262219	0.91[ASN][1000 genomes]
rs9468824	0.85[ASN][1000 genomes]
rs9968884	0.83[ASN][1000 genomes]
rs9968888	0.83[ASN][1000 genomes]
rs9968913	0.83[ASN][1000 genomes]
rs9968960	0.83[ASN][1000 genomes]
rs9969042	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv10812	chr6:30785661-30789859	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1264352	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30779000-30794800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:30779000-30795800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:30779200-30790000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:30782000-30796000	Weak transcription	Pancreas	Pancrea
5	chr6:30782000-30797000	Weak transcription	Gastric	stomach
6	chr6:30782400-30790000	Weak transcription	Primary T cells from cord blood	blood
7	chr6:30782600-30789800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:30782800-30794600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:30783200-30789800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:30783400-30794600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:30785400-30789800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:30785400-30790800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:30785600-30790000	Enhancers	HMEC	breast
14	chr6:30786200-30790000	Enhancers	K562	blood
15	chr6:30786200-30790800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:30786400-30790800	Enhancers	HSMMtube	muscle
17	chr6:30786400-30791400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:30786400-30792800	Enhancers	Stomach Mucosa	stomach
19	chr6:30786600-30789800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:30787200-30790000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:30787400-30792200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr6:30787600-30791000	Enhancers	Colonic Mucosa	Colon
23	chr6:30787800-30789800	Enhancers	NHEK	skin
24	chr6:30787800-30791400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:30788000-30790200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr6:30788200-30790000	Weak transcription	Fetal Stomach	stomach
27	chr6:30788200-30791400	Weak transcription	Thymus	Thymus
28	chr6:30788200-30792400	Weak transcription	Spleen	Spleen
29	chr6:30788200-30794800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:30788200-30794800	Weak transcription	Esophagus	oesophagus
31	chr6:30788400-30791000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:30788400-30795800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:30788400-30796000	Weak transcription	Lung	lung
34	chr6:30788600-30789800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:30788600-30789800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:30788600-30790000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:30788600-30790200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:30788600-30790200	Weak transcription	Right Atrium	heart
39	chr6:30788600-30790800	Enhancers	Hela-S3	cervix
40	chr6:30788600-30791400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:30788600-30794800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:30788600-30794800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:30788600-30795800	Weak transcription	Left Ventricle	heart
44	chr6:30788600-30795800	Weak transcription	Right Ventricle	heart
45	chr6:30788800-30795800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:30789200-30789800	Enhancers	HepG2	liver
47	chr6:30789200-30790000	Enhancers	GM12878-XiMat	blood
48	chr6:30789200-30790000	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:30789200-30790400	Enhancers	HUVEC	blood vessel
50	chr6:30789200-30791200	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links