Variant report

Variant	rs33635
Chromosome Location	chr16:11991944-11991945
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	chr16:11988100..11996073-chr16:12007143..12011577,10	MCF-7	breast:
2	chr16:11988764..11995180-chr16:12006980..12012068,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103342	Chromatin interaction
ENSG00000266163	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12597429	0.83[MEX][hapmap]
rs12924398	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12925740	0.81[EUR][1000 genomes]
rs154148	0.81[EUR][1000 genomes]
rs171656	0.81[EUR][1000 genomes]
rs190461	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2018199	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2075158	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2098722	0.84[EUR][1000 genomes]
rs251723	0.80[EUR][1000 genomes]
rs256400	0.86[EUR][1000 genomes]
rs28279	0.88[TSI][hapmap]
rs33619	0.88[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs33621	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33623	0.88[CEU][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs33624	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33629	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33630	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33631	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs33637	0.85[EUR][1000 genomes]
rs33638	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33640	0.85[EUR][1000 genomes]
rs33643	0.84[EUR][1000 genomes]
rs33645	0.80[EUR][1000 genomes]
rs33647	0.82[EUR][1000 genomes]
rs33648	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33649	0.83[EUR][1000 genomes]
rs33651	0.82[EUR][1000 genomes]
rs33652	0.82[EUR][1000 genomes]
rs33653	0.82[EUR][1000 genomes]
rs33654	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33655	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs33660	0.88[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs3850997	0.82[TSI][hapmap]
rs3971913	0.82[EUR][1000 genomes]
rs40311	0.88[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs42424	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4429311	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4493057	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4511557	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs4561483	0.95[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs456325	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7198817	0.81[CEU][hapmap]
rs7202234	0.88[CEU][hapmap]
rs8052900	0.86[EUR][1000 genomes]
rs8061189	0.88[CEU][hapmap];0.80[EUR][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	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv984257	chr16:11968206-11992901	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1735	chr16:11986963-12031597	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs33635	RSL1D1	cis	parietal	SCAN
rs33635	GSPT1	Cis_1M	lymphoblastoid	RTeQTL
rs33635	TNFRSF17	cis	cerebellum	SCAN
rs33635	TNFRSF17	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11962000-11992200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr16:11962000-11994600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr16:11962200-11992000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr16:11962400-11992000	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr16:11962400-11992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:11962400-11992200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr16:11962400-11992400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr16:11962400-11995000	Strong transcription	Dnd41	blood
9	chr16:11962600-12004000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr16:11965800-11995000	Strong transcription	HepG2	liver
11	chr16:11966200-12006200	Weak transcription	Fetal Heart	heart
12	chr16:11971600-11995000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr16:11976600-12004800	Weak transcription	Esophagus	oesophagus
14	chr16:11977000-12007200	Weak transcription	Colonic Mucosa	Colon
15	chr16:11977200-12004600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr16:11979800-12003200	Weak transcription	Small Intestine	intestine
17	chr16:11981200-12004000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr16:11981600-11994400	Weak transcription	Psoas Muscle	Psoas
19	chr16:11981800-12001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr16:11982000-12007400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr16:11984000-11992200	Strong transcription	NHEK	skin
22	chr16:11984200-11992000	Strong transcription	Hela-S3	cervix
23	chr16:11984400-11992200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr16:11984600-12006800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr16:11985000-11993400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr16:11985000-12007000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr16:11985600-11992000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr16:11986200-11993200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr16:11986200-11996400	Weak transcription	Spleen	Spleen
30	chr16:11986200-11999600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr16:11986200-12003800	Weak transcription	Brain Substantia Nigra	brain
32	chr16:11986400-11995600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr16:11986600-11992000	Strong transcription	Primary B cells from cord blood	blood
34	chr16:11987400-11994000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr16:11987600-12004000	Weak transcription	Brain Angular Gyrus	brain
36	chr16:11987800-11993200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr16:11987800-11993200	Weak transcription	Colon Smooth Muscle	Colon
38	chr16:11987800-11994400	Weak transcription	Stomach Mucosa	stomach
39	chr16:11987800-11994800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr16:11987800-11996600	Weak transcription	Right Ventricle	heart
41	chr16:11987800-12004200	Weak transcription	Fetal Brain Female	brain
42	chr16:11987800-12007600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr16:11987800-12008400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr16:11988000-11993000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr16:11988000-11993200	Weak transcription	Pancreas	Pancrea
46	chr16:11988000-12004200	Weak transcription	Fetal Kidney	kidney
47	chr16:11988200-11994400	Weak transcription	Gastric	stomach
48	chr16:11988200-12000000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr16:11989000-11993000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr16:11989000-11995000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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