Variant report

Variant	rs16872577
Chromosome Location	chr7:108139327-108139328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108136513..108141686-chr7:108208548..108212373,5	K562	blood:
2	chr7:108139312..108141712-chr7:108164785..108166455,2	K562	blood:
3	chr7:108137781..108139518-chr7:108153454..108155535,2	K562	blood:
4	chr7:108139312..108141712-chr7:108164785..108167554,3	K562	blood:

Variant related genes	Relation type
ENSG00000135241	Chromatin interaction
ENSG00000177683	Chromatin interaction
ENSG00000128590	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10487855	0.83[YRI][hapmap]
rs10953572	0.80[EUR][1000 genomes]
rs10953573	0.80[EUR][1000 genomes]
rs11971386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11977071	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs11983802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11983842	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12530879	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12531222	0.83[YRI][hapmap]
rs12536929	0.80[EUR][1000 genomes]
rs12538539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12540029	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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705474	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13239792	0.95[ASN][1000 genomes]
rs16872576	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17134769	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs34164886	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34459886	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34771129	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34827770	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34915298	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34959248	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35220845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35444439	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35687881	0.80[EUR][1000 genomes]
rs3752639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3763460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3763463	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60117684	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6964631	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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6980319	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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71568523	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71568524	0.83[EUR][1000 genomes]
rs71568525	0.83[EUR][1000 genomes]
rs71568529	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71568531	0.87[ASN][1000 genomes]
rs71568533	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7786180	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9641410	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9641411	0.90[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 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	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:108102400-108143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:108102800-108158400	Weak transcription	HSMMtube	muscle
4	chr7:108105800-108158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr7:108106200-108150800	Weak transcription	NHLF	lung
6	chr7:108107600-108141000	Weak transcription	Spleen	Spleen
7	chr7:108109000-108141400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:108109000-108162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:108109600-108140600	Weak transcription	Esophagus	oesophagus
10	chr7:108109600-108143400	Weak transcription	GM12878-XiMat	blood
11	chr7:108111400-108142200	Strong transcription	Liver	Liver
12	chr7:108111400-108154800	Weak transcription	NHEK	skin
13	chr7:108111600-108142600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:108111800-108143600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr7:108113200-108157000	Weak transcription	Psoas Muscle	Psoas
16	chr7:108113600-108140000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:108113800-108150800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr7:108113800-108165800	Weak transcription	Gastric	stomach
19	chr7:108114000-108139800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:108114000-108165000	Weak transcription	Colonic Mucosa	Colon
21	chr7:108114400-108160000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr7:108115200-108151800	Weak transcription	NHDF-Ad	bronchial
23	chr7:108116400-108141400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:108117200-108150600	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:108117200-108151800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:108117800-108164200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr7:108119200-108157600	Weak transcription	Brain Germinal Matrix	brain
28	chr7:108119800-108139800	Weak transcription	Brain Angular Gyrus	brain
29	chr7:108119800-108139800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr7:108119800-108140000	Weak transcription	Fetal Muscle Leg	muscle
31	chr7:108119800-108140200	Weak transcription	Brain Substantia Nigra	brain
32	chr7:108119800-108140600	Weak transcription	Lung	lung
33	chr7:108119800-108140600	Weak transcription	Ovary	ovary
34	chr7:108119800-108144200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:108119800-108144200	Weak transcription	Small Intestine	intestine
36	chr7:108119800-108151000	Weak transcription	Fetal Kidney	kidney
37	chr7:108119800-108151800	Weak transcription	Thymus	Thymus
38	chr7:108119800-108151800	Weak transcription	HMEC	breast
39	chr7:108119800-108154800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr7:108119800-108158200	Weak transcription	Aorta	Aorta
41	chr7:108121600-108158200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr7:108122000-108141200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr7:108122000-108144200	Weak transcription	Fetal Brain Male	brain
44	chr7:108122200-108141400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr7:108123400-108144800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:108126800-108140000	Weak transcription	Osteobl	bone
47	chr7:108127800-108140000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr7:108128000-108140600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr7:108128000-108141600	Weak transcription	Fetal Brain Female	brain
50	chr7:108128200-108158000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links