Variant report

Variant	rs643867
Chromosome Location	chr10:6209915-6209916
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	chr10:6208646..6210405-chr10:6219404..6221992,2	MCF-7	breast:
2	chr10:6193977..6196105-chr10:6208590..6211475,2	K562	blood:
3	chr10:6202871..6212786-chr10:6240811..6248696,29	MCF-7	breast:
4	chr10:6203753..6210403-chr10:6228380..6234446,7	MCF-7	breast:
5	chr10:6135493..6137735-chr10:6209780..6211467,2	K562	blood:
6	chr10:6197111..6199158-chr10:6208551..6211482,2	K562	blood:
7	chr10:6209809..6221866-chr10:6241112..6247882,17	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL2RA-5	chr10:6209362-6211035	l_249_chr10:6203492-6223680_skeltalMuscle

No data

Variant related genes	Relation type
ENSG00000213994	Chromatin interaction
ENSG00000170525	Chromatin interaction
ENSG00000263628	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12572233	0.86[EUR][1000 genomes]
rs12572255	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs602395	0.91[CHB][hapmap]
rs605015	0.85[EUR][1000 genomes]
rs609587	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613960	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629298	0.91[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641736	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642104	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643503	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs652318	0.95[CEU][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs653265	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654876	0.91[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs657523	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs657600	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs658386	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs668796	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669534	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7896238	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv894817	chr10:6173416-6251252	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6188400-6225200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:6206400-6210400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:6206600-6210200	Weak transcription	Esophagus	oesophagus
4	chr10:6206600-6210200	Weak transcription	Ovary	ovary
5	chr10:6206600-6220000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:6206800-6211200	Weak transcription	Aorta	Aorta
7	chr10:6206800-6211800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr10:6206800-6212600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr10:6206800-6213600	Weak transcription	HSMM	muscle
10	chr10:6207000-6210200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:6207000-6210400	Genic enhancers	Dnd41	blood
12	chr10:6207000-6211400	Weak transcription	Stomach Mucosa	stomach
13	chr10:6207000-6211800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr10:6207000-6212600	Weak transcription	NH-A	brain
15	chr10:6207000-6212800	Weak transcription	Osteobl	bone
16	chr10:6207000-6213400	Weak transcription	HSMMtube	muscle
17	chr10:6207000-6213800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:6207000-6213800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:6207000-6214000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:6207000-6214800	Weak transcription	Colonic Mucosa	Colon
21	chr10:6207000-6218600	Weak transcription	Fetal Lung	lung
22	chr10:6207000-6219000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr10:6207000-6219400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr10:6207000-6244400	Weak transcription	Hela-S3	cervix
25	chr10:6207200-6211800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:6207200-6214200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr10:6207200-6217800	Weak transcription	HMEC	breast
28	chr10:6207200-6218800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:6207400-6210600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr10:6207400-6211400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:6207400-6211800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:6207600-6210600	Weak transcription	Right Ventricle	heart
33	chr10:6207600-6211200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:6207600-6211400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr10:6207600-6211400	Weak transcription	HUVEC	blood vessel
36	chr10:6207600-6211600	Weak transcription	Liver	Liver
37	chr10:6207600-6211600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr10:6207600-6212600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr10:6207600-6212600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr10:6207600-6213400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr10:6207600-6213600	Weak transcription	Brain Angular Gyrus	brain
42	chr10:6207600-6213600	Weak transcription	Brain Substantia Nigra	brain
43	chr10:6207600-6214200	Weak transcription	Brain Germinal Matrix	brain
44	chr10:6207600-6214600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr10:6207600-6214800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr10:6207600-6218600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr10:6207800-6210200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr10:6207800-6210600	Genic enhancers	K562	blood
49	chr10:6207800-6210600	Strong transcription	NHEK	skin
50	chr10:6207800-6210800	Genic enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links