Variant report

Variant	rs9468333
Chromosome Location	chr6:28271198-28271199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28270484..28272247-chr6:28307860..28310847,2	K562	blood:
2	chr6:28270788..28272885-chr6:28303466..28306771,3	K562	blood:
3	chr6:28264442..28268560-chr6:28269964..28273646,5	K562	blood:
4	chr6:28270747..28272712-chr6:28309347..28312254,2	K562	blood:
5	chr6:28264329..28266427-chr6:28269486..28272144,3	K562	blood:
6	chr6:28268157..28273166-chr6:28302896..28306229,5	K562	blood:
7	chr6:28266856..28268560-chr6:28269964..28272119,2	K562	blood:
8	chr6:28261083..28263249-chr6:28270818..28273469,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:85)

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	0.83[AMR][1000 genomes]
rs1150679	0.83[AMR][1000 genomes]
rs1150686	0.83[AMR][1000 genomes]
rs1150690	0.81[AMR][1000 genomes]
rs1150694	1.00[YRI][hapmap]
rs1150705	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][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];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1150709	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.82[ASN][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];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1150716	0.93[AMR][1000 genomes];0.98[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];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[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];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[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];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[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];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11755942	0.83[CEU][hapmap]
rs12180820	0.81[TSI][hapmap];0.85[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];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1225618	0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs1225710	0.91[ASW][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1225715	0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs1233660	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233713	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][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];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13437294	0.82[CEU][hapmap]
rs1361385	0.83[CEU][hapmap]
rs1361386	0.85[EUR][1000 genomes]
rs1416918	0.83[CEU][hapmap]
rs1416920	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1531681	0.91[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[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];0.92[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[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];0.82[AMR][1000 genomes];0.83[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];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021826	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2041230	0.83[CEU][hapmap]
rs2071965	0.83[CEU][hapmap]
rs2108926	0.86[EUR][1000 genomes]
rs213228	0.83[CEU][hapmap]
rs213238	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs213240	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[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];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2394049	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2622320	1.00[YRI][hapmap]
rs2622322	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs2791333	0.81[ASW][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.83[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.85[EUR][1000 genomes]
rs707907	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]
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];0.88[AMR][1000 genomes];0.82[ASN][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];0.90[AMR][1000 genomes];0.96[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];0.98[AMR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];1.00[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];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9461456	0.83[CEU][hapmap]
rs9461458	0.83[CEU][hapmap]
rs9468344	0.83[TSI][hapmap];0.86[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
rs9468333	ZKSCAN3	cis	parietal	SCAN
rs9468333	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs9468333	NKAPL	cis	parietal	SCAN
rs9468333	BTN3A2	cis	parietal	SCAN
rs9468333	ZNF187	cis	cerebellum	SCAN
rs9468333	ZSCAN23	cis	cerebellum	SCAN
rs9468333	ZSCAN23	cis	Muscle Skeletal	GTEx
rs9468333	ZKSCAN3	cis	cerebellum	SCAN
rs9468333	ZSCAN23	cis	Artery Tibial	GTEx
rs9468333	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9468333	ZNF323	cis	parietal	SCAN
rs9468333	AL022393.7	cis	Muscle Skeletal	GTEx
rs9468333	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs9468333	RP5-874C20.3	cis	Thyroid	GTEx
rs9468333	ZSCAN23	cis	parietal	SCAN
rs9468333	ZNF192	cis	cerebellum	SCAN
rs9468333	AL022393.7	cis	Esophagus Muscularis	GTEx
rs9468333	ZSCAN31	cis	lung	GTEx
rs9468333	HIST1H1D	cis	parietal	SCAN
rs9468333	ZNF323	cis	cerebellum	SCAN
rs9468333	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs9468333	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs9468333	AL022393.7	cis	Nerve Tibial	GTEx
rs9468333	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs9468333	HIST1H2BO	cis	parietal	SCAN
rs9468333	AL022393.7	cis	Heart Left Ventricle	GTEx
rs9468333	ZSCAN31	cis	Thyroid	GTEx
rs9468333	ZSCAN31	cis	Stomach	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
2	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28250000-28293800	Weak transcription	Gastric	stomach
4	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
5	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:28255200-28271200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:28255200-28271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
14	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
15	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
17	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:28255400-28271200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:28255400-28278400	Weak transcription	HepG2	liver
20	chr6:28255600-28271400	Weak transcription	Placenta	Placenta
21	chr6:28255600-28272000	Weak transcription	Brain Substantia Nigra	brain
22	chr6:28256400-28271600	Weak transcription	Liver	Liver
23	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:28257600-28278800	Weak transcription	NHDF-Ad	bronchial
26	chr6:28257800-28279000	Weak transcription	HMEC	breast
27	chr6:28258400-28273800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:28258600-28273000	Weak transcription	Fetal Brain Male	brain
29	chr6:28264200-28273000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:28264200-28273000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:28264800-28272000	Weak transcription	HSMM	muscle
32	chr6:28264800-28274200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:28264800-28278600	Weak transcription	Fetal Intestine Small	intestine
34	chr6:28265000-28280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:28265400-28271400	Weak transcription	NHLF	lung
36	chr6:28265400-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:28265600-28274000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:28266400-28278800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:28266800-28273400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:28268000-28271200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:28268000-28272400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:28268400-28280600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:28268800-28274400	Weak transcription	Fetal Stomach	stomach
44	chr6:28268800-28293400	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:28269000-28274200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:28269200-28271400	Strong transcription	K562	blood
47	chr6:28269200-28275000	Weak transcription	Lung	lung
48	chr6:28269200-28278600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:28269200-28291600	Weak transcription	Right Ventricle	heart
50	chr6:28269400-28271600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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