Variant report

Variant	rs11259699
Chromosome Location	chr10:6625794-6625795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:16)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr10:6625311-6625889	K562	blood:	n/a	chr10:6625522-6625531 chr10:6625543-6625554 chr10:6625523-6625532 chr10:6625521-6625532
2	MYC	chr10:6625338-6625809	K562	blood:	n/a	chr10:6625561-6625570
3	MYC	chr10:6625371-6625960	K562	blood:	n/a	chr10:6625561-6625570
4	POLR2A	chr10:6625571-6625798	ProgFib	skin:	n/a	n/a
5	POLR2A	chr10:6625057-6626151	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL137145.1-2	chr10:6625638-6625994	XLOC_008370
2	lnc-AL137145.1-2	chr10:6625638-6627323	XLOC_008370
3	lnc-AL137145.1-2	chr10:6625638-6625880	XLOC_008370
4	lnc-AL137145.1-2	chr10:6625638-6627674	XLOC_008370
5	lnc-AL137145.1-2	chr10:6625641-6625880	XLOC_008370
6	lnc-AL137145.1-2	chr10:6625638-6625880	XLOC_008370
7	lnc-AL137145.1-2	chr10:6625638-6625880	XLOC_008370
8	lnc-AL137145.1-2	chr10:6625638-6625880	XLOC_008370
9	lnc-AL137145.1-2	chr10:6625638-6630358	XLOC_008370
10	lnc-AL137145.1-2	chr10:6625638-6625990	ENSG00000237943
11	lnc-AL137145.1-2	chr10:6625638-6626261	ENSG00000237943
12	lnc-AL137145.1-2	chr10:6625638-6625880	NONHSAT011229
13	lnc-PRKCQ-3	chr10:6625641-6626263	NONHSAT011234
14	lnc-AL137145.1-2	chr10:6625638-6627323	NONHSAT139952
15	lnc-AL137145.1-2	chr10:6625767-6625880	ENSG00000237943.2
16	lnc-AL137145.1-2	chr10:6625767-6626157	ENSG00000237943.2

No data

Variant related genes	Relation type
PRKCQ-AS1	TF binding region
PRKCQ	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12256539	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260151	1.00[EUR][1000 genomes]
rs4575169	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv549912	chr10:6566975-6629225	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription 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	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6623000-6627600	Weak transcription	Small Intestine	intestine
2	chr10:6623000-6633200	Weak transcription	Pancreas	Pancrea
3	chr10:6623000-6636400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:6623200-6631000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:6623400-6626000	Weak transcription	Fetal Stomach	stomach
6	chr10:6623400-6633600	Weak transcription	Primary B cells from cord blood	blood
7	chr10:6623400-6634800	Weak transcription	Fetal Intestine Small	intestine
8	chr10:6623600-6626400	Weak transcription	Fetal Kidney	kidney
9	chr10:6623600-6631000	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr10:6623800-6625800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr10:6623800-6627800	Weak transcription	HepG2	liver
12	chr10:6623800-6628200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr10:6623800-6634400	Weak transcription	NHEK	skin
14	chr10:6624000-6625800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:6624000-6628600	Weak transcription	Brain Anterior Caudate	brain
16	chr10:6624200-6625800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr10:6624200-6626000	Genic enhancers	Dnd41	blood
18	chr10:6624200-6631000	Weak transcription	Psoas Muscle	Psoas
19	chr10:6624200-6635000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr10:6624200-6635400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr10:6624200-6637000	Weak transcription	A549	lung
22	chr10:6624400-6626200	Genic enhancers	Fetal Thymus	thymus
23	chr10:6624400-6627600	Weak transcription	Brain Substantia Nigra	brain
24	chr10:6624400-6628800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr10:6624400-6629600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr10:6624400-6630200	Weak transcription	Brain Hippocampus Middle	brain
27	chr10:6624400-6633800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:6624600-6625800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr10:6624600-6628000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr10:6624800-6628800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr10:6624800-6635800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr10:6625000-6626000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr10:6625000-6626200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr10:6625000-6626400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr10:6625000-6627800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:6625000-6629200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:6625200-6626000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr10:6625200-6626000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr10:6625200-6626200	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr10:6625200-6626200	Strong transcription	Fetal Muscle Leg	muscle
41	chr10:6625200-6626400	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr10:6625200-6627200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr10:6625400-6626200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:6625400-6626200	Strong transcription	Fetal Intestine Large	intestine
45	chr10:6625400-6626200	Transcr. at gene 5' and 3'	K562	blood
46	chr10:6625400-6626400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:6625400-6627000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:6625400-6628200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:6625400-6628800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr10:6625600-6625800	Active TSS	Primary T helper naive cells from peripheral blood	blood

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