Variant report

Variant	rs6685043
Chromosome Location	chr1:173957513-173957514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173956360..173957903-chr1:173959725..173961914,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16846433	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs16846526	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16846546	0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs16846561	0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs16846593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2065170	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2068871	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs2146372	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2227589	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2227592	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2759328	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs58174255	0.97[ASN][1000 genomes]
rs58911640	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59393482	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60689957	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7516351	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7521960	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs941987	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs941988	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv872550	chr1:173913804-173964206	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6685043	RABGAP1L	cis	lymphoblastoid	seeQTL
rs6685043	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL
rs6685043	CENPL	cis	lymphoblastoid	seeQTL
rs6685043	dJ383J4.3	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173900000-173958600	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr1:173900000-173962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:173901400-173962200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:173901600-173966400	Strong transcription	Dnd41	blood
11	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:173905000-173962400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:173906000-173959000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:173906800-173959000	Strong transcription	Liver	Liver
15	chr1:173909800-173974200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:173915600-173977800	Weak transcription	Stomach Mucosa	stomach
17	chr1:173923400-173962400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:173929000-173962200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:173931200-173965600	Weak transcription	Small Intestine	intestine
22	chr1:173931200-173969800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:173941000-173965000	Strong transcription	Fetal Thymus	thymus
24	chr1:173941200-173958600	Strong transcription	Adipose Nuclei	Adipose
25	chr1:173942200-173967400	Weak transcription	Fetal Heart	heart
26	chr1:173942200-173986200	Weak transcription	Fetal Brain Male	brain
27	chr1:173945400-173958600	Strong transcription	HUVEC	blood vessel
28	chr1:173947000-173966000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:173949200-173970600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:173949400-173960000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:173949600-173965600	Weak transcription	Esophagus	oesophagus
32	chr1:173949600-173970600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:173950200-173958000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:173950200-173958400	Weak transcription	Spleen	Spleen
35	chr1:173950200-173961800	Weak transcription	Aorta	Aorta
36	chr1:173950400-173960200	Weak transcription	Brain Angular Gyrus	brain
37	chr1:173950600-173973400	Weak transcription	Psoas Muscle	Psoas
38	chr1:173951200-173958200	Weak transcription	Lung	lung
39	chr1:173951400-173960000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:173951400-173960200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:173951600-173958200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:173952000-173958200	Weak transcription	Gastric	stomach
43	chr1:173952200-173960000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:173952200-173967200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:173952800-173958200	Weak transcription	Left Ventricle	heart
46	chr1:173952800-173958200	Weak transcription	Thymus	Thymus
47	chr1:173952800-173958400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:173952800-173959800	Weak transcription	Right Ventricle	heart
49	chr1:173952800-173960000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:173952800-173960200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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