Variant report

Variant	rs9301
Chromosome Location	chr6:28292706-28292707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27805510..27808348-chr6:28291399..28294314,2	K562	blood:
2	chr6:28290697..28292824-chr6:28302762..28304976,2	MCF-7	breast:
3	chr6:28185352..28187060-chr6:28290813..28293732,2	K562	blood:
4	chr6:28278690..28281090-chr6:28292415..28293983,2	K562	blood:

Variant related genes	Relation type
ENSG00000184348	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1005125	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1052215	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10946954	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1124132	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1150668	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs1150670	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1150679	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1150686	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1150690	0.87[AMR][1000 genomes]
rs1150691	0.81[CEU][hapmap]
rs1150694	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1150705	0.86[CHB][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1150707	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1150709	0.96[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1150711	0.91[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs1150716	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150718	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1150721	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1150724	0.90[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1150726	0.90[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs12214383	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1225618	0.81[ASW][hapmap];0.92[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1225710	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1225715	0.81[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1233660	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1233713	0.96[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13408	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1531681	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1654774	0.84[CEU][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs1736891	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1736895	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1778484	0.90[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs1997660	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];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2021826	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2023493	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs213236	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs213237	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs213238	0.87[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs213240	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2142730	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247002	0.84[EUR][1000 genomes]
rs2394049	0.95[CHB][hapmap];0.80[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2531803	0.83[CHB][hapmap]
rs2531825	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs2531831	0.84[EUR][1000 genomes]
rs2531832	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2622320	0.92[CEU][hapmap]
rs2622322	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2791333	0.90[ASW][hapmap];0.92[CEU][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2859348	0.86[CHB][hapmap]
rs2859365	0.84[EUR][1000 genomes]
rs34024998	0.87[EUR][1000 genomes]
rs4455662	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4713158	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs707907	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]
rs7206	0.90[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs728122	0.84[EUR][1000 genomes]
rs853683	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];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs853684	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853690	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];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs853693	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];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs916403	0.83[CHB][hapmap]
rs9368565	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9468333	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];0.90[AMR][1000 genomes];0.96[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:33)

SNP	Gene	Cis/trans	Tissue	Source
rs9301	ZNF323	cis	cerebellum	SCAN
rs9301	ZKSCAN3	cis	cerebellum	SCAN
rs9301	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs9301	AL022393.7	cis	Muscle Skeletal	GTEx
rs9301	ZSCAN23	cis	parietal	SCAN
rs9301	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs9301	ZSCAN31	cis	lung	GTEx
rs9301	AL022393.7	cis	Esophagus Muscularis	GTEx
rs9301	ZSCAN23	cis	Muscle Skeletal	GTEx
rs9301	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs9301	ZKSCAN3	cis	parietal	SCAN
rs9301	AL022393.7	cis	Artery Tibial	GTEx
rs9301	AL022393.7	cis	Nerve Tibial	GTEx
rs9301	ZNF323	cis	Cerebellum	GTEx
rs9301	AL022393.7	cis	Heart Left Ventricle	GTEx
rs9301	ZSCAN31	cis	Thyroid	GTEx
rs9301	AL022393.7	cis	Artery Aorta	GTEx
rs9301	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs9301	ZSCAN31	cis	Muscle Skeletal	GTEx
rs9301	ZNF323	cis	parietal	SCAN
rs9301	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs9301	RP5-874C20.3	cis	Thyroid	GTEx
rs9301	ZSCAN23	cis	Artery Tibial	GTEx
rs9301	ZSCAN23	cis	cerebellum	SCAN
rs9301	ZNF192	cis	cerebellum	SCAN
rs9301	ZSCAN31	cis	Stomach	GTEx
rs9301	AL022393.7	cis	lung	GTEx
rs9301	ZNF323	cis	Frontal Cortex	GTEx
rs9301	ZNF323	cis	Temporal Cortex	GTEx
rs9301	ZSCAN23	cis	lung	GTEx
rs9301	ZNF187	cis	cerebellum	SCAN
rs9301	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs9301	NKAPL	cis	parietal	SCAN

Chromatin state (count:48 , 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	chr6:28270000-28293400	Weak transcription	Brain Angular Gyrus	brain
5	chr6:28271200-28293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:28271400-28293400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:28272400-28293200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:28279400-28293800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:28281200-28293600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:28288200-28299200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:28288800-28293600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:28289200-28293600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:28289600-28293200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:28290000-28293600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:28290200-28293600	Weak transcription	Colonic Mucosa	Colon
16	chr6:28290600-28295800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
17	chr6:28290800-28293000	Strong transcription	Fetal Stomach	stomach
18	chr6:28290800-28298200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr6:28291400-28295600	ZNF genes & repeats	Ovary	ovary
20	chr6:28291400-28298000	ZNF genes & repeats	Liver	Liver
21	chr6:28291600-28293400	Strong transcription	Fetal Brain Female	brain
22	chr6:28291600-28294000	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr6:28291600-28295600	ZNF genes & repeats	Psoas Muscle	Psoas
24	chr6:28291600-28295600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
25	chr6:28291600-28295600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
26	chr6:28291600-28296000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:28291800-28292800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:28291800-28293800	Strong transcription	Brain Hippocampus Middle	brain
29	chr6:28291800-28295600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
30	chr6:28292000-28295800	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr6:28292200-28292800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:28292200-28293000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:28292200-28293000	Enhancers	HepG2	liver
34	chr6:28292200-28293600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:28292200-28293600	Weak transcription	Brain Anterior Caudate	brain
36	chr6:28292200-28293600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr6:28292200-28293800	Weak transcription	Pancreas	Pancrea
38	chr6:28292200-28294000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:28292200-28294000	Weak transcription	Aorta	Aorta
40	chr6:28292200-28294000	Weak transcription	Lung	lung
41	chr6:28292400-28292800	Weak transcription	Left Ventricle	heart
42	chr6:28292400-28292800	Weak transcription	Right Ventricle	heart
43	chr6:28292400-28293600	Strong transcription	Fetal Heart	heart
44	chr6:28292600-28293800	Strong transcription	Brain Germinal Matrix	brain
45	chr6:28292600-28295600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
46	chr6:28292600-28295600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr6:28292600-28295600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
48	chr6:28292600-28297200	ZNF genes & repeats	Stomach Smooth Muscle	stomach

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