Variant report

Variant	rs1225710
Chromosome Location	chr6:28100640-28100641
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28100227-28100847	K562	blood:	n/a	n/a
2	POLR2A	chr6:28099946-28101087	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:28100552-28100853	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:28100637-28101088	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:28100129-28101487	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr6:28100590-28101059	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27870902..27873198-chr6:28100520..28102131,2	K562	blood:
2	chr6:28100206..28102984-chr6:28103490..28105139,2	MCF-7	breast:
3	chr6:28100159..28103502-chr6:28106801..28111190,4	MCF-7	breast:
4	chr6:28098585..28101126-chr6:28317174..28319178,2	K562	blood:
5	chr6:27859270..27861304-chr6:28100599..28103889,3	K562	blood:
6	chr6:28100317..28107200-chr6:28184436..28191088,8	MCF-7	breast:
7	chr6:28099723..28110178-chr6:28301599..28306918,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261839	TF binding region
ENSG00000269293	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000176933	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 34 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1150668	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1150670	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150679	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150686	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150690	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1150691	0.83[CEU][hapmap]
rs1150694	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1150705	0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1150707	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1150709	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1150711	0.86[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap]
rs1150716	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1150718	1.00[YRI][hapmap]
rs1150721	1.00[YRI][hapmap]
rs1150724	0.91[ASW][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs1150726	0.91[ASW][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs12214383	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1225618	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1225715	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]
rs1233660	0.86[AFR][1000 genomes]
rs1233713	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12530158	0.86[JPT][hapmap]
rs13408	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs149956	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs149963	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs149971	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap]
rs149976	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes]
rs1531681	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs156737	0.85[AFR][1000 genomes]
rs1654774	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1736891	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1736895	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1778484	0.91[ASW][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap]
rs1997660	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]
rs2021826	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203878	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];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213240	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2142730	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2394049	0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2622320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2622322	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2791333	0.90[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713158	0.83[AMR][1000 genomes]
rs707907	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]
rs7206	0.91[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs853683	0.91[ASW][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs853684	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs853690	0.91[ASW][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs853693	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]
rs9301	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]
rs9468333	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]

mRNA abundance (count:34)

SNP	Gene	Cis/trans	Tissue	Source
rs1225710	ZSCAN23	cis	cerebellum	SCAN
rs1225710	ZSCAN31	cis	lung	GTEx
rs1225710	AL022393.7	cis	Artery Aorta	GTEx
rs1225710	AL022393.7	cis	lung	GTEx
rs1225710	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1225710	ZSCAN31	cis	Thyroid	GTEx
rs1225710	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1225710	ZNF323	cis	Frontal Cortex	GTEx
rs1225710	ZSCAN23	cis	Artery Tibial	GTEx
rs1225710	BTN3A3	cis	parietal	SCAN
rs1225710	AL022393.7	cis	Muscle Skeletal	GTEx
rs1225710	ZNF323	cis	parietal	SCAN
rs1225710	ZNF323	cis	cerebellum	SCAN
rs1225710	ZSCAN23	cis	lung	GTEx
rs1225710	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs1225710	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1225710	ZSCAN23	cis	lymphoblastoid	seeQTL
rs1225710	RP5-874C20.3	cis	Thyroid	GTEx
rs1225710	ZSCAN23	cis	Muscle Skeletal	GTEx
rs1225710	AL022393.7	cis	Artery Tibial	GTEx
rs1225710	ZNF323	cis	brain	seeQTL
rs1225710	AL022393.7	cis	Nerve Tibial	GTEx
rs1225710	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1225710	ZKSCAN3	cis	cerebellum	SCAN
rs1225710	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1225710	ZNF187	cis	cerebellum	SCAN
rs1225710	ZSCAN23	cis	parietal	SCAN
rs1225710	ZNF323	cis	Cerebellum	GTEx
rs1225710	ZNF192	cis	cerebellum	SCAN
rs1225710	NKAPL	cis	parietal	SCAN
rs1225710	HIST1H3I	cis	cerebellum	SCAN
rs1225710	ZKSCAN3	cis	parietal	SCAN
rs1225710	ZNF323	cis	Temporal Cortex	GTEx
rs1225710	ZNF323	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28092800-28101800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28092800-28103800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28092800-28103800	Weak transcription	Ovary	ovary
4	chr6:28092800-28104000	Weak transcription	Aorta	Aorta
5	chr6:28092800-28104000	Weak transcription	Small Intestine	intestine
6	chr6:28092800-28104200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:28093000-28100800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:28093000-28103200	Weak transcription	NHLF	lung
9	chr6:28093000-28103800	Weak transcription	Psoas Muscle	Psoas
10	chr6:28093000-28104000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:28093000-28104200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:28093200-28102400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:28093200-28103200	Weak transcription	HMEC	breast
14	chr6:28093200-28103600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:28093400-28102600	Weak transcription	NHDF-Ad	bronchial
16	chr6:28093400-28103200	Weak transcription	NHEK	skin
17	chr6:28093400-28103400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:28093600-28101200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:28093600-28101200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:28093600-28101400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:28093600-28102200	Weak transcription	Brain Substantia Nigra	brain
22	chr6:28093600-28102600	Weak transcription	Right Ventricle	heart
23	chr6:28093600-28103200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:28093600-28103200	Weak transcription	Right Atrium	heart
25	chr6:28093600-28104000	Weak transcription	Fetal Intestine Small	intestine
26	chr6:28093600-28104200	Weak transcription	Pancreas	Pancrea
27	chr6:28093600-28104400	Weak transcription	Esophagus	oesophagus
28	chr6:28093600-28104400	Weak transcription	Gastric	stomach
29	chr6:28093800-28101400	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr6:28093800-28101600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:28093800-28101600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:28093800-28102600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:28093800-28103200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:28093800-28104000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:28093800-28104200	Weak transcription	Lung	lung
36	chr6:28094000-28101000	Strong transcription	Fetal Muscle Leg	muscle
37	chr6:28094000-28101400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:28094200-28101000	Strong transcription	Primary B cells from cord blood	blood
39	chr6:28094400-28101800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:28094400-28104000	Weak transcription	Colonic Mucosa	Colon
41	chr6:28094600-28103200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:28094800-28101800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:28094800-28102200	Strong transcription	Primary T cells from cord blood	blood
44	chr6:28095000-28101600	Weak transcription	Fetal Brain Male	brain
45	chr6:28095200-28101200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:28095200-28103200	Weak transcription	Osteobl	bone
47	chr6:28095600-28103200	Weak transcription	Fetal Kidney	kidney
48	chr6:28095600-28103400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr6:28095800-28103200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:28096600-28102600	Genic enhancers	K562	blood

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