Variant report

Variant	rs853685
Chromosome Location	chr6:28288785-28288786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr6:28288536-28288932	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28288486..28291463-chr6:28293519..28295323,2	K562	blood:
2	chr6:28110255..28111827-chr6:28288667..28290240,2	K562	blood:
3	chr6:27863775..27866407-chr6:28287805..28289740,2	K562	blood:
4	chr6:28287491..28290035-chr6:28302948..28305431,2	K562	blood:
5	chr6:28285662..28290423-chr6:28300603..28305447,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270326	TF binding region
ENSG00000235109	Chromatin interaction
ENSG00000238610	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 15 )

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];0.91[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];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13200462	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[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];0.91[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];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1679732	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[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];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1778511	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1936365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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];0.90[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2743555	0.91[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];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799079	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68141011	0.91[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	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6920512	0.82[CHB][hapmap]
rs735765	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs7740487	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs853676	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]
rs853678	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853681	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853682	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853687	0.91[ASN][1000 genomes]
rs853688	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs853694	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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	0.90[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs853685	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs853685	OR2B8P	cis	Thyroid	GTEx
rs853685	HIST1H4F	cis	parietal	SCAN
rs853685	BTN2A1	cis	parietal	SCAN
rs853685	ZNF323	cis	parietal	SCAN
rs853685	ZNF192	cis	cerebellum	SCAN
rs853685	LRRC16A	cis	parietal	SCAN
rs853685	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs853685	ZSCAN23	cis	parietal	SCAN
rs853685	HIST1H2BC	cis	parietal	SCAN
rs853685	ZSCAN23	cis	cerebellum	SCAN
rs853685	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs853685	AL022393.7	cis	Muscle Skeletal	GTEx
rs853685	RP5-874C20.3	cis	Thyroid	GTEx
rs853685	HIST1H4L	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28250000-28293800	Weak transcription	Gastric	stomach
2	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:28268800-28293400	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:28269200-28291600	Weak transcription	Right Ventricle	heart
5	chr6:28270000-28290400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:28270000-28291400	Weak transcription	Ovary	ovary
7	chr6:28270000-28291600	Weak transcription	Brain Anterior Caudate	brain
8	chr6:28270000-28291600	Weak transcription	Fetal Brain Female	brain
9	chr6:28270000-28293400	Weak transcription	Brain Angular Gyrus	brain
10	chr6:28271200-28293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:28271400-28293400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:28272400-28291800	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:28272400-28293200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:28272600-28292000	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:28272600-28292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:28272600-28292600	Weak transcription	Brain Germinal Matrix	brain
17	chr6:28273000-28291600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:28279400-28290600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:28279400-28293800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:28281200-28290800	Weak transcription	Fetal Stomach	stomach
21	chr6:28281200-28290800	Weak transcription	Left Ventricle	heart
22	chr6:28281200-28291600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:28281200-28291600	Weak transcription	Pancreas	Pancrea
24	chr6:28281200-28293600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:28288200-28288800	ZNF genes & repeats	Aorta	Aorta
26	chr6:28288200-28299200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:28288400-28288800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr6:28288600-28288800	ZNF genes & repeats	Psoas Muscle	Psoas
29	chr6:28288600-28289600	ZNF genes & repeats	Stomach Smooth Muscle	stomach

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