Variant report

Variant	rs4552702
Chromosome Location	chr6:88298414-88298415
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:88298309-88298532	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:88274592..88276563-chr6:88297497..88299608,2	MCF-7	breast:
2	chr6:88298133..88299802-chr6:88410474..88412513,2	MCF-7	breast:
3	chr6:88277452..88280023-chr6:88298199..88301235,3	MCF-7	breast:

Variant related genes	Relation type
ORC3	TF binding region
ENSG00000146282	Chromatin interaction
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11965607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12663400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13213729	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13220363	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35773999	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4330517	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707380	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7748693	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7756133	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7768566	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7772351	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs910267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444515	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444529	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450725	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450727	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450730	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450731	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450756	0.82[CHB][hapmap]
rs9450757	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450759	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450765	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][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	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4552702	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs4552702	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
2	chr6:88274800-88298800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:88283000-88298600	Weak transcription	Aorta	Aorta
4	chr6:88289200-88298600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:88289800-88298800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:88291800-88298800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:88293800-88298600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:88295800-88298600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr6:88296000-88298600	Enhancers	Psoas Muscle	Psoas
10	chr6:88296200-88298600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:88296800-88298600	Enhancers	Left Ventricle	heart
12	chr6:88296800-88298800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr6:88297000-88298600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:88297400-88298800	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:88297400-88298800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:88297400-88299000	Flanking Active TSS	Dnd41	blood
17	chr6:88297600-88298600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:88297600-88298600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:88297600-88298600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:88297600-88298600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr6:88297600-88298800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:88297600-88299000	Enhancers	Small Intestine	intestine
23	chr6:88297800-88298600	Enhancers	Primary B cells from cord blood	blood
24	chr6:88297800-88298600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:88297800-88298600	Flanking Active TSS	HepG2	liver
26	chr6:88297800-88298800	Flanking Active TSS	Osteobl	bone
27	chr6:88297800-88299200	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr6:88297800-88301200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr6:88297800-88301400	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr6:88298000-88298600	Flanking Active TSS	K562	blood
31	chr6:88298000-88298800	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr6:88298000-88298800	Flanking Active TSS	Fetal Intestine Small	intestine
33	chr6:88298000-88298800	Flanking Active TSS	HUVEC	blood vessel
34	chr6:88298000-88299000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr6:88298000-88299000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:88298000-88299200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr6:88298000-88300600	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr6:88298000-88300800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:88298000-88301000	Active TSS	HSMM	muscle
40	chr6:88298000-88301400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:88298000-88301400	Active TSS	A549	lung
42	chr6:88298200-88298600	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr6:88298200-88298600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:88298200-88298600	Enhancers	Fetal Heart	heart
45	chr6:88298200-88298600	Enhancers	Placenta	Placenta
46	chr6:88298200-88298600	Flanking Active TSS	Ovary	ovary
47	chr6:88298200-88298600	Flanking Active TSS	HMEC	breast
48	chr6:88298200-88298800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr6:88298200-88298800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:88298200-88298800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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