Variant report

Variant	rs6924902
Chromosome Location	chr6:13789155-13789156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13788072..13790327-chr6:13790683..13792361,2	K562	blood:
2	chr6:13615016..13616949-chr6:13788580..13791434,2	MCF-7	breast:
3	chr6:13711228..13713635-chr6:13789081..13791410,2	MCF-7	breast:
4	chr6:13710394..13713005-chr6:13788901..13792554,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC90A-8	chr6:13786977-13790645	NONHSAT107814

Variant related genes	Relation type
ENSG00000010017	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1204144	0.89[ASN][1000 genomes]
rs13204134	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207837	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219011	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16874314	0.81[YRI][hapmap]
rs35048447	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36030296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36030644	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62387427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6941754	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13766800-13802400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:13768800-13790400	Weak transcription	Lung	lung
3	chr6:13773200-13790200	Weak transcription	Spleen	Spleen
4	chr6:13780600-13790000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:13780600-13790000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:13780800-13789200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:13780800-13797800	Weak transcription	Thymus	Thymus
8	chr6:13781000-13801200	Weak transcription	Psoas Muscle	Psoas
9	chr6:13781000-13802000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:13781200-13790400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:13781400-13791800	Weak transcription	HSMM	muscle
12	chr6:13781600-13789200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:13782000-13790000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:13782600-13789800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:13782800-13790000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:13783800-13790200	Weak transcription	Pancreas	Pancrea
17	chr6:13784600-13792000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:13784600-13794600	Weak transcription	A549	lung
19	chr6:13785000-13790000	Weak transcription	K562	blood
20	chr6:13785000-13800800	Weak transcription	Brain Angular Gyrus	brain
21	chr6:13785200-13801600	Weak transcription	Gastric	stomach
22	chr6:13785400-13800600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:13786000-13789200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:13786000-13789800	Weak transcription	Primary T cells from cord blood	blood
25	chr6:13786000-13789800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:13786000-13789800	Weak transcription	HepG2	liver
27	chr6:13786000-13790000	Weak transcription	Liver	Liver
28	chr6:13786000-13801200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:13786400-13790000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:13786400-13790000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:13786400-13794800	Weak transcription	NHLF	lung
32	chr6:13786600-13790200	Weak transcription	Fetal Intestine Small	intestine
33	chr6:13786800-13790200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:13787000-13790000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr6:13787000-13794400	Weak transcription	HMEC	breast
36	chr6:13787200-13789800	Weak transcription	NHEK	skin
37	chr6:13787200-13790200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr6:13787200-13792400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:13787400-13790400	Weak transcription	Fetal Stomach	stomach
40	chr6:13787400-13790600	Strong transcription	Primary B cells from cord blood	blood
41	chr6:13787400-13794400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:13787400-13794400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:13787400-13794600	Strong transcription	Fetal Intestine Large	intestine
44	chr6:13787400-13794600	Strong transcription	Dnd41	blood
45	chr6:13787600-13792200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:13787600-13799400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:13787800-13789800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:13787800-13790000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr6:13787800-13790200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:13787800-13790200	Weak transcription	Brain Cingulate Gyrus	brain

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