Variant report

Variant	rs11207998
Chromosome Location	chr1:63091471-63091472
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:63081752..63083296-chr1:63090887..63092573,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10158897	1.00[JPT][hapmap]
rs10159255	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10458569	0.83[CHB][hapmap]
rs10493322	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10789113	0.86[ASN][1000 genomes]
rs10789118	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10789119	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10789120	0.91[ASN][1000 genomes]
rs10889333	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10889334	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10889335	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10889338	0.84[ASN][1000 genomes]
rs10889342	0.80[ASN][1000 genomes]
rs10889348	0.89[ASN][1000 genomes]
rs10889352	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10889353	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11207977	0.84[ASN][1000 genomes]
rs11207980	0.86[ASN][1000 genomes]
rs11207981	0.81[JPT][hapmap]
rs11207982	0.86[ASN][1000 genomes]
rs11207992	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11207995	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11207996	0.89[ASN][1000 genomes]
rs11208004	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11485618	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1168023	0.81[JPT][hapmap]
rs1168030	0.81[JPT][hapmap]
rs1168086	0.88[JPT][hapmap]
rs12024419	0.82[CHB][hapmap]
rs12025714	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12027778	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12030293	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038768	0.89[ASN][1000 genomes]
rs12039115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12041843	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12042319	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12043877	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12043910	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12047226	0.91[ASN][1000 genomes]
rs12048208	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12116574	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12136083	1.00[JPT][hapmap]
rs12239736	0.89[ASN][1000 genomes]
rs1570694	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1781221	0.81[JPT][hapmap]
rs2029763	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34152715	0.89[ASN][1000 genomes]
rs3850634	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3913007	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4350231	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4587594	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs56115463	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61775910	0.82[ASN][1000 genomes]
rs638305	0.81[JPT][hapmap]
rs641540	0.81[JPT][hapmap]
rs995000	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs998403	0.85[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817371	chr1:62901935-63129697	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1014376	chr1:62976472-63181359	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv870559	chr1:63057136-63113719	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1000988	chr1:63061791-63107526	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11207998	DOCK7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63007200-63096200	Weak transcription	HUVEC	blood vessel
2	chr1:63036800-63113600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:63038400-63095600	Weak transcription	Brain Germinal Matrix	brain
4	chr1:63039200-63095200	Weak transcription	Ovary	ovary
5	chr1:63041000-63095200	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:63041000-63095600	Weak transcription	Fetal Stomach	stomach
7	chr1:63051800-63096000	Weak transcription	Left Ventricle	heart
8	chr1:63066800-63112200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:63068400-63095200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:63072000-63095800	Weak transcription	Primary T cells from cord blood	blood
11	chr1:63074400-63095600	Weak transcription	Fetal Intestine Small	intestine
12	chr1:63074400-63099000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:63075200-63095200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:63075400-63095600	Weak transcription	Fetal Brain Female	brain
15	chr1:63075400-63095600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:63075600-63095600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:63075600-63106600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:63075800-63095800	Weak transcription	Aorta	Aorta
19	chr1:63075800-63099000	Weak transcription	Fetal Brain Male	brain
20	chr1:63076400-63097000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:63077400-63095200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:63079200-63098800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:63079200-63099000	Weak transcription	Brain Angular Gyrus	brain
24	chr1:63079600-63095800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:63079600-63095800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:63079800-63108800	Weak transcription	Primary B cells from cord blood	blood
27	chr1:63080000-63095800	Weak transcription	NH-A	brain
28	chr1:63082200-63099200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:63082200-63121000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:63082400-63098800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:63082800-63132600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:63083000-63095600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:63083000-63096000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr1:63083200-63095600	Weak transcription	Esophagus	oesophagus
35	chr1:63083400-63095600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:63083400-63119000	Weak transcription	Fetal Thymus	thymus
37	chr1:63084000-63095000	Weak transcription	Fetal Lung	lung
38	chr1:63084000-63095600	Weak transcription	Brain Anterior Caudate	brain
39	chr1:63084200-63094800	Weak transcription	Dnd41	blood
40	chr1:63084200-63095000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:63084600-63095600	Weak transcription	NHLF	lung
42	chr1:63084800-63095200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:63084800-63096000	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:63084800-63121000	Weak transcription	Small Intestine	intestine
45	chr1:63085400-63095200	Weak transcription	Adipose Nuclei	Adipose
46	chr1:63085400-63113600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:63085800-63093800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:63085800-63095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:63085800-63095600	Weak transcription	Fetal Intestine Large	intestine
50	chr1:63085800-63095600	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links