Variant report

Variant	rs16894171
Chromosome Location	chr6:28602272-28602273
allele	A/G
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	NFIC	chr6:28602233-28602746	ECC-1	luminal epithelium:	n/a	n/a
2	GATA3	chr6:28602159-28602495	SH-SY5Y	brain:	n/a	chr6:28602396-28602405
3	MXI1	chr6:28602158-28604100	SK-N-SH	brain:	n/a	n/a
4	ZNF263	chr6:28601986-28604212	HEK293-T-REx	kidney:	n/a	n/a
5	REST	chr6:28602233-28603859	H1-neurons	neurons:	n/a	chr6:28603707-28603717
6	NFIC	chr6:28602149-28602921	ECC-1	luminal epithelium:	n/a	n/a
7	KAP1	chr6:28601523-28602919	U2OS	brain:	n/a	n/a
8	KAP1	chr6:28601225-28603443	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28582156..28586237-chr6:28601069..28603430,3	K562	blood:
2	chr6:28598566..28600689-chr6:28601579..28603852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271440	TF binding region
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10738069	0.87[EUR][1000 genomes]
rs10807035	0.80[EUR][1000 genomes]
rs10807039	0.87[EUR][1000 genomes]
rs12662929	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16894166	0.97[ASN][1000 genomes]
rs16894169	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894191	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2057296	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4711173	0.82[ASN][1000 genomes]
rs4711178	0.87[AFR][1000 genomes]
rs4713173	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713175	0.89[AFR][1000 genomes]
rs4947335	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55776584	0.89[AFR][1000 genomes]
rs55963280	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56227726	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58490223	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62402376	0.82[ASN][1000 genomes]
rs62402378	0.87[ASN][1000 genomes]
rs62402390	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62402392	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62402394	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62402400	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62406542	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62406553	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6456824	0.85[ASN][1000 genomes]
rs6942252	0.88[ASN][1000 genomes]
rs72850099	0.97[ASN][1000 genomes]
rs732395	0.87[EUR][1000 genomes]
rs7743296	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7746909	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7748225	0.85[EUR][1000 genomes]
rs7760867	0.87[EUR][1000 genomes]
rs7767144	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295775	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16894171	BTN3A3	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28601000-28604000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:28601200-28603200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28601200-28603800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:28601200-28603800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:28601200-28604000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:28601400-28602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:28601400-28602400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:28601400-28602600	Weak transcription	Pancreas	Pancrea
9	chr6:28601400-28604000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr6:28601600-28603600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:28601600-28604200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:28602000-28602400	Flanking Active TSS	Fetal Brain Male	brain
13	chr6:28602000-28602400	Bivalent Enhancer	Fetal Intestine Large	intestine
14	chr6:28602200-28602400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:28602200-28602400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:28602200-28602400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:28602200-28602400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
18	chr6:28602200-28602400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:28602200-28602400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
20	chr6:28602200-28602400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:28602200-28602400	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr6:28602200-28602400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr6:28602200-28602400	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr6:28602200-28602400	Bivalent Enhancer	NHEK	skin
25	chr6:28602200-28602600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr6:28602200-28602600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:28602200-28602600	Flanking Active TSS	Fetal Brain Female	brain
28	chr6:28602200-28602600	Flanking Bivalent TSS/Enh	Fetal Heart	heart
29	chr6:28602200-28602600	Bivalent Enhancer	Fetal Intestine Small	intestine
30	chr6:28602200-28602600	Flanking Active TSS	Fetal Kidney	kidney
31	chr6:28602200-28603200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr6:28602200-28603600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:28602200-28604000	Active TSS	Brain Anterior Caudate	brain
34	chr6:28602200-28604000	Active TSS	A549	lung
35	chr6:28602200-28604000	Flanking Bivalent TSS/Enh	HepG2	liver
36	chr6:28602200-28604200	Bivalent/Poised TSS	Brain Angular Gyrus	brain

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