Variant report

Variant	rs16860418
Chromosome Location	chr2:173317753-173317754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173317241..173319524-chr2:173329311..173331759,2	K562	blood:
2	chr2:173314991..173316624-chr2:173316906..173318533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232788	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16860448	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16860527	0.86[ASW][hapmap]
rs16860635	0.83[LWK][hapmap]
rs28703731	1.00[AMR][1000 genomes]
rs3934627	0.81[YRI][hapmap]
rs61318391	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7564174	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7594126	1.00[YRI][hapmap];0.97[AFR][1000 genomes];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:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173307200-173318600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:173307400-173322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:173307600-173321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:173310400-173318000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr2:173310800-173318200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:173310800-173318600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:173310800-173319800	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:173310800-173320000	Weak transcription	Lung	lung
9	chr2:173310800-173322400	Weak transcription	Thymus	Thymus
10	chr2:173311400-173318000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr2:173311600-173319000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:173311600-173319200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:173311600-173319200	Weak transcription	HUVEC	blood vessel
14	chr2:173311800-173319200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:173312200-173319400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:173312200-173323600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:173312400-173319200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:173313200-173319800	Weak transcription	Fetal Kidney	kidney
19	chr2:173313600-173323400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:173313800-173319200	Weak transcription	HepG2	liver
21	chr2:173314000-173318600	Weak transcription	Colonic Mucosa	Colon
22	chr2:173314200-173319200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:173314200-173319200	Weak transcription	Hela-S3	cervix
24	chr2:173314400-173318600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:173314400-173319400	Weak transcription	Fetal Intestine Small	intestine
26	chr2:173314800-173319000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:173315000-173317800	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr2:173315000-173320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:173315000-173320800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:173315200-173318000	Weak transcription	Small Intestine	intestine
31	chr2:173315200-173318200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr2:173315200-173319400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:173315200-173324800	Genic enhancers	NHEK	skin
34	chr2:173315400-173319800	Weak transcription	HSMM	muscle
35	chr2:173315400-173320200	Weak transcription	HSMMtube	muscle
36	chr2:173316000-173320400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:173316000-173320800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr2:173316000-173322800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr2:173316200-173317800	Enhancers	Duodenum Mucosa	Duodenum
40	chr2:173316200-173320800	Genic enhancers	HMEC	breast
41	chr2:173316200-173321800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:173316200-173321800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr2:173316200-173323400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:173316200-173323800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:173316400-173317800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr2:173316400-173317800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:173316400-173317800	Enhancers	Right Atrium	heart
48	chr2:173316400-173318400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:173316400-173318600	Enhancers	Adipose Nuclei	Adipose
50	chr2:173316400-173319400	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links