Variant report

Variant	rs16846809
Chromosome Location	chr1:174219398-174219399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174208598..174210493-chr1:174218021..174220094,2	MCF-7	breast:
2	chr1:174215485..174217028-chr1:174218870..174220698,2	MCF-7	breast:
3	chr1:174217947..174220664-chr1:174222845..174224894,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10489254	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489261	0.83[AFR][1000 genomes]
rs16846769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846815	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs57425860	0.83[EUR][1000 genomes]
rs58525721	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs58657641	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58911640	0.91[AFR][1000 genomes]
rs59061054	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59949376	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6668618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698964	0.91[AFR][1000 genomes]
rs7516351	0.80[AFR][1000 genomes]
rs7549724	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008993	chr1:174180019-174331358	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv528675	chr1:174195629-174219398	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv872553	chr1:174195629-174373379	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv872554	chr1:174209978-174291950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv3453880	chr1:174218725-174221815	Strong transcription Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv3453881	chr1:174218725-174221815	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16846809	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL
rs16846809	CENPL	cis	lymphoblastoid	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174176000-174222400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:174176800-174222400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:174186800-174232000	Weak transcription	HSMMtube	muscle
4	chr1:174189000-174232000	Weak transcription	HSMM	muscle
5	chr1:174191400-174232000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:174191600-174232200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:174192000-174219400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:174192400-174224600	Weak transcription	Fetal Thymus	thymus
9	chr1:174200800-174249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:174201000-174221800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:174201000-174249800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:174201200-174221400	Weak transcription	NHDF-Ad	bronchial
13	chr1:174202400-174221400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:174202400-174224800	Weak transcription	Fetal Intestine Large	intestine
15	chr1:174202400-174225400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:174202400-174229400	Weak transcription	Fetal Lung	lung
17	chr1:174202400-174232200	Weak transcription	Right Ventricle	heart
18	chr1:174202400-174256800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:174208400-174219800	Weak transcription	Esophagus	oesophagus
20	chr1:174208600-174249200	Weak transcription	Placenta	Placenta
21	chr1:174208800-174221800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:174208800-174222200	Weak transcription	NHEK	skin
23	chr1:174209600-174223200	Weak transcription	A549	lung
24	chr1:174209800-174221400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:174211200-174258200	Weak transcription	Dnd41	blood
26	chr1:174211600-174231600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:174212400-174227600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:174213800-174232200	Weak transcription	Aorta	Aorta
29	chr1:174213800-174249800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:174213800-174258600	Weak transcription	K562	blood
31	chr1:174214000-174225200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:174214000-174239200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:174214200-174220800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr1:174214200-174224800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:174214200-174249400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:174214200-174249800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:174214400-174221800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:174214400-174222200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:174214400-174222800	Weak transcription	Primary T cells from cord blood	blood
40	chr1:174214400-174225600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:174214400-174232000	Weak transcription	Lung	lung
42	chr1:174214400-174232000	Weak transcription	Ovary	ovary
43	chr1:174214400-174238000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:174214400-174249000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:174214400-174250000	Weak transcription	Adipose Nuclei	Adipose
46	chr1:174214400-174250600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:174214600-174222200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:174214600-174225000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:174214600-174231600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:174214600-174232000	Weak transcription	Fetal Stomach	stomach

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