Variant report

Variant	rs6682835
Chromosome Location	chr1:169847487-169847488
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169846979..169849303-chr1:169851464..169854908,3	K562	blood:
2	chr1:169798250..169800377-chr1:169845673..169848267,2	K562	blood:
3	chr1:169846941..169849701-chr1:169857998..169859525,2	MCF-7	breast:
4	chr1:169845717..169848182-chr1:169860925..169862962,2	MCF-7	breast:
5	chr1:169846456..169849390-chr1:169863296..169865489,2	MCF-7	breast:
6	chr1:169846082..169850359-chr1:169859892..169864668,5	K562	blood:
7	chr1:169847146..169850317-chr1:169850331..169854277,4	K562	blood:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10733054	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs10737549	0.95[CEU][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10737550	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10737551	0.86[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10800479	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10800480	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10800481	0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800483	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10800484	0.81[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10800485	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10800486	0.96[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10919239	0.95[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs10919245	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10919248	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10919251	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10919257	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10919263	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12047487	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs12133843	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12724797	0.83[CEU][hapmap]
rs1883436	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2056980	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2056981	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2179396	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2205851	0.82[EUR][1000 genomes]
rs2281039	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2294322	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2294496	0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2420512	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2420514	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2491087	0.91[EUR][1000 genomes]
rs2491088	0.84[CEU][hapmap]
rs2750016	0.88[CEU][hapmap]
rs2806386	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2806393	0.88[CEU][hapmap]
rs2901179	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3753308	1.00[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3766132	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3766134	1.00[CEU][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3766137	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3766142	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766144	0.90[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3766148	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766151	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766154	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766155	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs4141917	0.84[CEU][hapmap]
rs4376791	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4508080	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4614317	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4615900	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4656196	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4656197	0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4656199	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4656200	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4656721	0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4656724	0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4656725	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6427217	0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs6427220	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6427224	0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6427225	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6427226	0.84[CHB][hapmap];0.90[JPT][hapmap];0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6427227	0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6427228	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656965	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6664099	0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6668114	0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6669794	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6670818	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6671752	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6676810	0.82[EUR][1000 genomes]
rs6680508	0.92[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs6680650	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6680938	0.84[AFR][1000 genomes]
rs6682137	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6683056	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684481	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6687377	0.95[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6702969	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs717481	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs732185	0.92[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7519364	0.84[ASN][1000 genomes]
rs7525259	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7526261	0.82[EUR][1000 genomes]
rs7530237	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7545011	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9287097	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6682835	C1orf112	Cis_1M	lymphoblastoid	RTeQTL
rs6682835	SCYL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
4	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr1:169814800-169848000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:169815200-169848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:169817800-169848600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr1:169818200-169847800	Strong transcription	Adipose Nuclei	Adipose
10	chr1:169819000-169848200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:169820600-169847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:169820600-169847800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:169820600-169848400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:169820600-169848600	Strong transcription	Fetal Lung	lung
15	chr1:169826800-169848600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:169831800-169848400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:169833800-169860200	Weak transcription	HMEC	breast
18	chr1:169837400-169848000	Strong transcription	Brain Anterior Caudate	brain
19	chr1:169841800-169848200	Strong transcription	Placenta	Placenta
20	chr1:169841800-169848400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:169841800-169848400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:169841800-169848600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:169841800-169848600	Strong transcription	Fetal Muscle Leg	muscle
24	chr1:169842000-169848000	Strong transcription	Thymus	Thymus
25	chr1:169842000-169848400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:169842000-169848400	Strong transcription	Fetal Thymus	thymus
27	chr1:169842000-169848600	Strong transcription	Fetal Intestine Large	intestine
28	chr1:169842200-169857400	Weak transcription	Fetal Brain Male	brain
29	chr1:169842400-169847800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:169842400-169848400	Strong transcription	Dnd41	blood
31	chr1:169842400-169848800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:169842400-169850800	Weak transcription	Esophagus	oesophagus
33	chr1:169842400-169851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:169842400-169851000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:169842400-169855600	Weak transcription	Brain Angular Gyrus	brain
36	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:169842600-169847800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:169842600-169854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:169843000-169847800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:169843000-169850200	Weak transcription	Colonic Mucosa	Colon
41	chr1:169843000-169851000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:169843200-169848000	Strong transcription	Spleen	Spleen
43	chr1:169843200-169848600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:169843400-169847800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:169843600-169848400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:169843600-169855000	Weak transcription	NHEK	skin
47	chr1:169843800-169847800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr1:169843800-169847800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:169843800-169848000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:169843800-169848000	Strong transcription	GM12878-XiMat	blood

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