Variant report

Variant	rs16860530
Chromosome Location	chr2:173349882-173349883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:173349780-173349930	BJ	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173345647..173349906-chr2:173350221..173353831,5	K562	blood:

Variant related genes	Relation type
ITGA6	TF binding region
ENSG00000091409	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16860433	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860453	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860500	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860505	1.00[AMR][1000 genomes]
rs16860517	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860562	1.00[AMR][1000 genomes]
rs16860566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860616	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16860730	1.00[AMR][1000 genomes]
rs2293645	1.00[ASW][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs28653613	1.00[AMR][1000 genomes]
rs34599583	1.00[AMR][1000 genomes]
rs59970483	0.86[AFR][1000 genomes]
rs73023431	1.00[AMR][1000 genomes]
rs73023468	1.00[AMR][1000 genomes]
rs73023472	1.00[AMR][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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173327200-173353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:173328800-173353400	Weak transcription	Right Ventricle	heart
5	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
6	chr2:173330200-173350400	Weak transcription	Primary B cells from cord blood	blood
7	chr2:173330400-173360400	Weak transcription	Small Intestine	intestine
8	chr2:173330600-173351400	Weak transcription	Psoas Muscle	Psoas
9	chr2:173330600-173351400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:173330600-173351600	Weak transcription	Brain Anterior Caudate	brain
11	chr2:173330600-173352400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:173330600-173352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:173330600-173352600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:173330600-173353200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:173330600-173353200	Weak transcription	Aorta	Aorta
16	chr2:173330600-173353400	Weak transcription	Fetal Stomach	stomach
17	chr2:173330600-173371400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:173330600-173372200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:173330600-173373200	Strong transcription	NHEK	skin
20	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
24	chr2:173331000-173370000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:173331000-173373800	Strong transcription	HMEC	breast
28	chr2:173331200-173372000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:173331400-173370200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:173332400-173351400	Weak transcription	Spleen	Spleen
31	chr2:173335400-173354000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:173337800-173360200	Strong transcription	Fetal Thymus	thymus
33	chr2:173342600-173353600	Weak transcription	A549	lung
34	chr2:173343000-173360200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:173343800-173351800	Weak transcription	Liver	Liver
36	chr2:173344000-173356000	Weak transcription	Fetal Kidney	kidney
37	chr2:173344400-173352600	Weak transcription	Brain Germinal Matrix	brain
38	chr2:173345200-173350000	Genic enhancers	Primary T cells from cord blood	blood
39	chr2:173345400-173351600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:173345400-173353000	Weak transcription	Lung	lung
41	chr2:173345600-173353600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:173345800-173350400	Strong transcription	HSMMtube	muscle
43	chr2:173345800-173359800	Weak transcription	Placenta	Placenta
44	chr2:173345800-173360800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr2:173346000-173350000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:173346000-173351400	Weak transcription	Adipose Nuclei	Adipose
47	chr2:173346000-173352000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:173346000-173352800	Weak transcription	NH-A	brain
49	chr2:173346000-173354200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:173346000-173360800	Strong transcription	HSMM	muscle

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