Variant report

Variant	rs1684898
Chromosome Location	chr10:61630250-61630251
allele	A/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:61628076..61632189-chr10:61632717..61638646,7	K562	blood:
2	chr10:61629487..61632652-chr10:61653201..61655969,3	K562	blood:
3	chr10:61630214..61632918-chr10:61637567..61639312,2	MCF-7	breast:
4	chr10:61611168..61612736-chr10:61629304..61631288,2	K562	blood:
5	chr10:61630078..61632932-chr10:61659731..61661689,2	MCF-7	breast:
6	chr10:61628363..61632189-chr10:61637394..61643761,6	K562	blood:
7	chr10:61628053..61631509-chr10:61662158..61666953,4	K562	blood:
8	chr10:61593326..61595203-chr10:61629041..61631124,2	K562	blood:
9	chr10:61628330..61633371-chr10:61664622..61667776,4	MCF-7	breast:
10	chr10:61628499..61631972-chr10:61632717..61636046,5	K562	blood:
11	chr10:61629487..61631429-chr10:61653201..61655597,2	K562	blood:
12	chr10:61623680..61630815-chr10:61664299..61668134,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10509114	0.87[MEX][hapmap];0.82[EUR][1000 genomes]
rs1171787	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1171820	0.89[GIH][hapmap]
rs1171833	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1180657	0.80[GIH][hapmap]
rs1184089	0.89[GIH][hapmap]
rs12776024	0.85[CHB][hapmap]
rs1624715	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1627130	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1627152	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1628136	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664258	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664260	0.93[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664261	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664262	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664263	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1684900	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1684902	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684903	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684914	0.85[JPT][hapmap]
rs17202600	0.87[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17790901	0.81[MEX][hapmap]
rs17791484	0.87[MEX][hapmap]
rs1972950	0.81[MEX][hapmap];0.82[TSI][hapmap]
rs2440906	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440908	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440909	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440910	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440911	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440918	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2450468	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2450469	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450471	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3763743	0.87[CEU][hapmap]
rs3763745	0.87[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs3793866	0.81[CEU][hapmap]
rs4146652	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4948249	0.83[CEU][hapmap]
rs61848704	0.81[EUR][1000 genomes]
rs61848705	0.81[EUR][1000 genomes]
rs895243	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1684898	SLC16A9	cis	cerebellum	SCAN
rs1684898	CCDC6	cis	cerebellum	SCAN
rs1684898	PHLDB3	trans	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61583200-61640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:61608000-61637200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:61618000-61632600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr10:61618600-61633200	Weak transcription	HSMM	muscle
5	chr10:61624200-61630400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:61624400-61630400	Enhancers	Pancreas	Pancrea
7	chr10:61624400-61632000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr10:61624600-61631200	Weak transcription	Fetal Lung	lung
9	chr10:61624800-61633000	Weak transcription	Brain Germinal Matrix	brain
10	chr10:61624800-61641000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr10:61625000-61632000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr10:61625000-61632000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr10:61625000-61632600	Weak transcription	Ovary	ovary
14	chr10:61625000-61638800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:61625000-61655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:61625200-61631600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr10:61625200-61632000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:61625200-61639200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr10:61625400-61631600	Weak transcription	Primary B cells from cord blood	blood
20	chr10:61625400-61631600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr10:61625600-61631400	Weak transcription	GM12878-XiMat	blood
22	chr10:61625600-61631600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr10:61625800-61632600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr10:61626000-61631600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr10:61626000-61631800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:61626000-61632200	Weak transcription	NHEK	skin
27	chr10:61626000-61632400	Weak transcription	Adipose Nuclei	Adipose
28	chr10:61626200-61631400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr10:61626400-61631400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:61626400-61632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:61626600-61631800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr10:61626800-61630400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr10:61626800-61631400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:61627000-61631600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:61627000-61632600	Weak transcription	Brain Substantia Nigra	brain
36	chr10:61627400-61630400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr10:61627800-61630400	Enhancers	Duodenum Mucosa	Duodenum
38	chr10:61628000-61630600	Enhancers	Gastric	stomach
39	chr10:61628000-61630800	Enhancers	Brain Anterior Caudate	brain
40	chr10:61628400-61630800	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr10:61628400-61632400	Enhancers	Colon Smooth Muscle	Colon
42	chr10:61628600-61631400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr10:61628600-61632800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr10:61628600-61632800	Enhancers	K562	blood
45	chr10:61628600-61638600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr10:61628800-61630600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr10:61628800-61630600	Weak transcription	Fetal Thymus	thymus
48	chr10:61628800-61632000	Weak transcription	Fetal Muscle Leg	muscle
49	chr10:61628800-61632000	Weak transcription	Spleen	Spleen
50	chr10:61628800-61632600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links