Variant report

Variant	rs707907
Chromosome Location	chr6:28291240-28291241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28289244..28291635-chr6:28299932..28302110,2	MCF-7	breast:
2	chr6:28288486..28291463-chr6:28293519..28295323,2	K562	blood:
3	chr6:28290697..28292824-chr6:28302762..28304976,2	MCF-7	breast:
4	chr6:28185352..28187060-chr6:28290813..28293732,2	K562	blood:
5	chr6:28281200..28284924-chr6:28289065..28292211,3	K562	blood:
6	chr6:28281200..28284127-chr6:28290711..28292363,2	K562	blood:

Variant related genes	Relation type
ENSG00000176933	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1005125	1.00[YRI][hapmap]
rs1052215	0.91[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1054372	0.83[CEU][hapmap]
rs1150670	0.80[AMR][1000 genomes]
rs1150679	0.80[AMR][1000 genomes]
rs1150686	0.80[AMR][1000 genomes]
rs1150694	1.00[YRI][hapmap]
rs1150705	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs1150707	0.91[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs1150709	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs1150711	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1150716	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1150718	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1150721	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150724	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150726	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11755942	0.83[CEU][hapmap]
rs12180820	0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12214383	0.91[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs1225618	0.96[MEX][hapmap];0.86[TSI][hapmap]
rs1225710	0.91[ASW][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1225715	0.86[TSI][hapmap]
rs1233660	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233713	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12697938	0.83[CEU][hapmap]
rs13408	0.91[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13437294	0.82[CEU][hapmap]
rs1361385	0.83[CEU][hapmap]
rs1361386	0.84[EUR][1000 genomes]
rs1416918	0.83[CEU][hapmap]
rs1416920	0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs1531681	0.91[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs1558205	0.87[CEU][hapmap]
rs1591913	0.83[CEU][hapmap]
rs1654774	0.88[MEX][hapmap];0.81[MKK][hapmap]
rs16894060	0.83[CEU][hapmap]
rs1736891	0.91[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs1736895	0.91[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs1778484	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1997660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2021826	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2041230	0.83[CEU][hapmap]
rs2071965	0.83[CEU][hapmap]
rs2108926	0.85[EUR][1000 genomes]
rs213228	0.83[CEU][hapmap]
rs213238	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs213240	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2142730	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2394049	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2622320	1.00[YRI][hapmap]
rs2622322	1.00[YRI][hapmap]
rs2791333	0.81[ASW][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs2859348	0.91[CHB][hapmap]
rs3734563	0.83[CEU][hapmap]
rs3800328	0.83[CEU][hapmap]
rs4254981	0.83[CEU][hapmap]
rs4357130	0.83[CEU][hapmap]
rs4713158	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456815	0.85[EUR][1000 genomes]
rs6899389	0.83[CEU][hapmap]
rs6907950	0.83[CEU][hapmap]
rs6908137	0.83[CEU][hapmap]
rs6922169	0.83[CEU][hapmap]
rs6922374	0.82[CEU][hapmap]
rs6928773	0.83[CEU][hapmap]
rs6942030	0.84[EUR][1000 genomes]
rs7206	0.82[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs758398	0.83[EUR][1000 genomes]
rs7759191	0.83[CEU][hapmap]
rs7764722	0.83[CEU][hapmap]
rs7772827	0.84[EUR][1000 genomes]
rs853683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853684	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs853690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301	0.90[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9461456	0.83[CEU][hapmap]
rs9461458	0.83[CEU][hapmap]
rs9468333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468344	0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs9468355	0.83[CEU][hapmap]
rs9468357	0.83[CEU][hapmap]
rs9468368	0.83[CEU][hapmap]
rs9468370	0.83[CEU][hapmap]

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:28)

SNP	Gene	Cis/trans	Tissue	Source
rs707907	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs707907	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs707907	ZKSCAN3	cis	cerebellum	SCAN
rs707907	ZNF192	cis	cerebellum	SCAN
rs707907	ZSCAN31	cis	lung	GTEx
rs707907	HIST1H1D	cis	parietal	SCAN
rs707907	ZSCAN31	cis	Stomach	GTEx
rs707907	NKAPL	cis	parietal	SCAN
rs707907	ZSCAN23	cis	Muscle Skeletal	GTEx
rs707907	HIST1H2BO	cis	parietal	SCAN
rs707907	AL022393.7	cis	Esophagus Muscularis	GTEx
rs707907	AL022393.7	cis	Muscle Skeletal	GTEx
rs707907	BTN3A2	cis	parietal	SCAN
rs707907	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs707907	AL022393.7	cis	Nerve Tibial	GTEx
rs707907	ZNF323	cis	parietal	SCAN
rs707907	ZNF187	cis	cerebellum	SCAN
rs707907	ZNF323	cis	cerebellum	SCAN
rs707907	ZKSCAN3	cis	parietal	SCAN
rs707907	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs707907	AL022393.7	cis	Heart Left Ventricle	GTEx
rs707907	ZSCAN23	cis	cerebellum	SCAN
rs707907	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs707907	ZSCAN23	cis	Artery Tibial	GTEx
rs707907	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs707907	ZSCAN23	cis	parietal	SCAN
rs707907	RP5-874C20.3	cis	Thyroid	GTEx
rs707907	ZSCAN31	cis	Thyroid	GTEx

Chromatin state (count:39 , 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	chr6:28270000-28291400	Weak transcription	Ovary	ovary
6	chr6:28270000-28291600	Weak transcription	Brain Anterior Caudate	brain
7	chr6:28270000-28291600	Weak transcription	Fetal Brain Female	brain
8	chr6:28270000-28293400	Weak transcription	Brain Angular Gyrus	brain
9	chr6:28271200-28293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:28271400-28293400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:28272400-28291800	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:28272400-28293200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:28272600-28292000	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:28272600-28292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:28272600-28292600	Weak transcription	Brain Germinal Matrix	brain
16	chr6:28273000-28291600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:28279400-28293800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:28281200-28291600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:28281200-28291600	Weak transcription	Pancreas	Pancrea
20	chr6:28281200-28293600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:28288200-28299200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:28288800-28293600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:28289200-28293600	Weak transcription	Brain Substantia Nigra	brain
24	chr6:28289600-28292600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr6:28289600-28293200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:28289800-28291400	Enhancers	HepG2	liver
27	chr6:28289800-28292200	ZNF genes & repeats	Aorta	Aorta
28	chr6:28290000-28293600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:28290200-28293600	Weak transcription	Colonic Mucosa	Colon
30	chr6:28290400-28291600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:28290400-28291600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:28290600-28291600	Weak transcription	Lung	lung
33	chr6:28290600-28295800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
34	chr6:28290800-28292400	Weak transcription	Fetal Heart	heart
35	chr6:28290800-28292400	Strong transcription	Left Ventricle	heart
36	chr6:28290800-28293000	Strong transcription	Fetal Stomach	stomach
37	chr6:28290800-28298200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr6:28291200-28291400	Weak transcription	Liver	Liver
39	chr6:28291200-28291800	Weak transcription	Duodenum Mucosa	Duodenum

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