Variant report

Variant	rs853676
Chromosome Location	chr6:28299687-28299688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28104111..28106206-chr6:28296771..28301344,4	K562	blood:
2	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
3	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
4	chr6:28265276..28267226-chr6:28297300..28300691,3	MCF-7	breast:
5	chr6:28271589..28273882-chr6:28298871..28300680,2	K562	blood:
6	chr6:28273496..28275716-chr6:28299383..28301919,2	K562	blood:

Variant related genes	Relation type
ENSG00000198315	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000261839	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10456362	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1076639	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11755032	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11965538	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13200462	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1339899	0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1419183	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1679709	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1679732	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1778507	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1778508	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1778511	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1936365	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs213239	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs213241	0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs213243	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs213244	0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2232427	0.80[CEU][hapmap]
rs2743554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[ASN][1000 genomes]
rs2743555	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799077	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799079	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68141011	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6901575	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs6905391	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6920512	0.82[CHB][hapmap]
rs735765	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs7740487	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs853678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853679	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853681	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853682	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853685	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853687	0.91[ASN][1000 genomes]
rs853688	1.00[ASN][1000 genomes]
rs853694	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9295765	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9366717	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs9380069	0.91[GIH][hapmap]
rs9393908	0.88[JPT][hapmap]
rs9461446	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9461448	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9461449	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9468321	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9468322	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9468342	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9468345	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9986596	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs853676	ZNF192	cis	cerebellum	SCAN
rs853676	ZNF323	cis	parietal	SCAN
rs853676	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs853676	BTN2A1	cis	parietal	SCAN
rs853676	HIST1H4L	cis	parietal	SCAN
rs853676	OR2B8P	cis	Thyroid	GTEx
rs853676	HIST1H4F	cis	parietal	SCAN
rs853676	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs853676	ZSCAN23	cis	cerebellum	SCAN
rs853676	HIST1H2BC	cis	parietal	SCAN
rs853676	AL022393.7	cis	Muscle Skeletal	GTEx
rs853676	ZSCAN23	cis	parietal	SCAN
rs853676	LRRC16A	cis	parietal	SCAN
rs853676	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28294800-28302000	Weak transcription	HepG2	liver
2	chr6:28294800-28302800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:28295400-28301400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:28295400-28302400	Weak transcription	Brain Angular Gyrus	brain
5	chr6:28295400-28302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:28295400-28303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:28295400-28303000	Weak transcription	Thymus	Thymus
8	chr6:28295600-28302000	Weak transcription	Fetal Heart	heart
9	chr6:28295600-28302200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:28295600-28302200	Weak transcription	Hela-S3	cervix
11	chr6:28295600-28302400	Weak transcription	Brain Substantia Nigra	brain
12	chr6:28295600-28302600	Weak transcription	Stomach Mucosa	stomach
13	chr6:28295600-28302800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:28295600-28302800	Weak transcription	Fetal Brain Male	brain
15	chr6:28295800-28302800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:28297000-28302000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:28297000-28302800	Weak transcription	Colonic Mucosa	Colon
18	chr6:28297000-28303400	Weak transcription	Gastric	stomach
19	chr6:28297200-28300400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:28297200-28302200	Weak transcription	Brain Anterior Caudate	brain
21	chr6:28297200-28302200	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:28297200-28302400	Weak transcription	Adipose Nuclei	Adipose
23	chr6:28297200-28302400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:28297200-28302400	Weak transcription	Pancreas	Pancrea
25	chr6:28297200-28302400	Weak transcription	Right Ventricle	heart
26	chr6:28297200-28302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:28297200-28302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:28297200-28302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:28297200-28302800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:28297200-28302800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:28297200-28302800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:28297200-28303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:28297400-28301400	Weak transcription	Lung	lung
34	chr6:28297400-28301800	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:28297400-28302200	Weak transcription	Fetal Brain Female	brain
36	chr6:28297400-28302400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:28297400-28302400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:28297400-28302400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:28297400-28302400	Weak transcription	Fetal Stomach	stomach
40	chr6:28297400-28302400	Weak transcription	Left Ventricle	heart
41	chr6:28297400-28302400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:28297400-28302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:28297400-28302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:28297400-28302800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:28297400-28302800	Weak transcription	Fetal Intestine Large	intestine
46	chr6:28297400-28302800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:28297400-28302800	Weak transcription	Psoas Muscle	Psoas
48	chr6:28297400-28303400	Weak transcription	Ovary	ovary
49	chr6:28297400-28303400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:28297600-28302200	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links