Variant report

Variant	rs1225715
Chromosome Location	chr6:28113373-28113374
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
2	chr6:28077736..28080081-chr6:28112119..28113939,2	K562	blood:
3	chr6:28112424..28114351-chr6:28312409..28315217,2	K562	blood:
4	chr6:27860855..27863824-chr6:28111543..28113437,2	K562	blood:
5	chr6:28086053..28088186-chr6:28111853..28113998,2	MCF-7	breast:
6	chr6:28108554..28111385-chr6:28111459..28116285,4	MCF-7	breast:
7	chr6:28113361..28114931-chr6:28160000..28161674,2	MCF-7	breast:
8	chr6:28108043..28113786-chr6:28190485..28194607,10	K562	blood:
9	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196331	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000198315	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 22 )

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

rs_ID	r²[population]
rs1150668	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1150670	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150679	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150686	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150690	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1150691	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs1150694	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150705	0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1150707	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1150709	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1150711	0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs1150716	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1150724	0.83[TSI][hapmap]
rs1150726	0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs12214383	0.83[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs1225618	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1225710	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233713	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12530158	0.81[JPT][hapmap]
rs13408	0.83[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs149956	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs149963	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149971	0.83[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs149976	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap]
rs1531681	0.83[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs1654774	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1736891	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1736895	0.83[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs1778484	0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs1997660	0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs2021826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203878	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs213240	0.80[AMR][1000 genomes]
rs2142730	0.96[CEU][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2394049	0.90[JPT][hapmap]
rs2622320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2622322	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2791333	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713158	0.82[AMR][1000 genomes]
rs707907	0.86[TSI][hapmap]
rs7206	0.96[CEU][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs853683	0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs853684	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs853690	0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs853693	0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs9301	0.81[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9468333	0.86[TSI][hapmap];0.82[AMR][1000 genomes]

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1225715	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1225715	AL022393.7	cis	Artery Tibial	GTEx
rs1225715	RP5-874C20.3	cis	Thyroid	GTEx
rs1225715	AL022393.7	cis	lung	GTEx
rs1225715	ZNF323	cis	multi-tissue	Pritchard
rs1225715	AL022393.7	cis	Muscle Skeletal	GTEx
rs1225715	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1225715	ZSCAN31	cis	lung	GTEx
rs1225715	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1225715	AL022393.7	cis	Nerve Tibial	GTEx
rs1225715	ZSCAN23	cis	Artery Tibial	GTEx
rs1225715	AL022393.7	cis	Artery Aorta	GTEx
rs1225715	ZNF323	cis	Cerebellum	GTEx
rs1225715	ZSCAN23	cis	Muscle Skeletal	GTEx
rs1225715	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1225715	ZNF323	cis	Temporal Cortex	GTEx
rs1225715	ZNF323	cis	Frontal Cortex	GTEx
rs1225715	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs1225715	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1225715	ZSCAN23	cis	lung	GTEx
rs1225715	ZNF323	cis	brain	seeQTL
rs1225715	ZSCAN31	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28110000-28116200	Weak transcription	Spleen	Spleen
2	chr6:28110200-28115800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:28110200-28115800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:28110200-28116000	Weak transcription	Lung	lung
5	chr6:28110200-28116200	Weak transcription	Esophagus	oesophagus
6	chr6:28110200-28116200	Weak transcription	Gastric	stomach
7	chr6:28110200-28116200	Weak transcription	Pancreas	Pancrea
8	chr6:28110200-28116200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:28110200-28120800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:28110600-28115600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:28110600-28115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28110600-28115800	Weak transcription	Left Ventricle	heart
13	chr6:28110600-28115800	Weak transcription	Thymus	Thymus
14	chr6:28110600-28116000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:28110600-28116000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:28110800-28115600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:28111000-28113400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:28111000-28115400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:28111000-28115800	Weak transcription	Fetal Stomach	stomach
20	chr6:28111000-28116000	Weak transcription	HMEC	breast
21	chr6:28111000-28120800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:28111200-28113400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:28111200-28113400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:28111200-28113400	Weak transcription	Fetal Kidney	kidney
25	chr6:28111200-28113400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:28111200-28113400	Weak transcription	NH-A	brain
27	chr6:28111200-28113400	Weak transcription	NHEK	skin
28	chr6:28111200-28115200	Weak transcription	Fetal Brain Female	brain
29	chr6:28111200-28115400	Weak transcription	NHLF	lung
30	chr6:28111200-28115600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:28111200-28115600	Weak transcription	Colonic Mucosa	Colon
32	chr6:28111200-28115600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:28111200-28115800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:28111200-28115800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:28111200-28115800	Weak transcription	Brain Angular Gyrus	brain
36	chr6:28111200-28116200	Weak transcription	Brain Anterior Caudate	brain
37	chr6:28111200-28116200	Weak transcription	Brain Substantia Nigra	brain
38	chr6:28111200-28116200	Weak transcription	Right Ventricle	heart
39	chr6:28111200-28116600	Weak transcription	Fetal Heart	heart
40	chr6:28111200-28119400	Weak transcription	Stomach Mucosa	stomach
41	chr6:28111200-28119600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:28111400-28113600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:28111400-28115400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:28111400-28115600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:28111400-28115600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:28111400-28115800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:28111400-28115800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr6:28111400-28116000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:28111400-28116000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:28111400-28116200	Weak transcription	Fetal Intestine Small	intestine

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