Variant report

Variant	rs1225618
Chromosome Location	chr6:28129713-28129714
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr6:28129490-28129785	Hela-S3	cervix:	n/a	n/a
2	TAF7	chr6:28129272-28129871	H1-hESC	embryonic stem cell:	n/a	n/a
3	MTA3	chr6:28129150-28129862	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:28129207-28130008	GM19099	blood:	n/a	n/a
5	POLR2A	chr6:28129199-28129821	HEK293	kidney:	n/a	n/a
6	POLR2A	chr6:28129302-28129783	HepG2	liver:	n/a	n/a
7	GABPA	chr6:28129081-28130063	HL-60	blood:	n/a	n/a
8	POLR2A	chr6:28129328-28129835	GM12892	blood:	n/a	n/a
9	POLR2A	chr6:28129155-28129842	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:28129068-28130016	HL-60	blood:	n/a	n/a
11	IRF1	chr6:28129394-28129731	K562	blood:	n/a	chr6:28129491-28129505
12	POLR2A	chr6:28129160-28129900	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr6:28126889-28129797	HepG2	liver:	n/a	n/a
14	POLR2A	chr6:28129274-28129751	GM12878	blood:	n/a	n/a
15	MAX	chr6:28129281-28129777	H1-hESC	embryonic stem cell:	n/a	n/a
16	TEAD4	chr6:28129219-28129820	K562	blood:	n/a	chr6:28129677-28129686
17	TAF1	chr6:28129287-28129737	ECC-1	luminal epithelium:	n/a	n/a
18	RAD21	chr6:28129290-28129766	SK-N-SH_RA	brain:	n/a	chr6:28129694-28129706
19	POLR2A	chr6:28129112-28129876	GM12892	blood:	n/a	n/a
20	MXI1	chr6:28129304-28129779	H1-hESC	embryonic stem cell:	n/a	chr6:28129445-28129454
21	E2F6	chr6:28129279-28129811	A549	lung:	n/a	chr6:28129490-28129500
22	POLR2A	chr6:28129217-28129795	HUVEC	blood vessel:	n/a	n/a
23	SPI1	chr6:28129334-28129727	HL-60	blood:	n/a	n/a
24	POLR2A	chr6:28129177-28129995	H1-hESC	embryonic stem cell:	n/a	n/a
25	SRF	chr6:28129351-28129753	GM12878	blood:	n/a	n/a
26	IRF1	chr6:28129297-28129780	K562	blood:	n/a	chr6:28129491-28129505
27	USF2	chr6:28129286-28130066	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:28129214-28129803	GM18951	blood:	n/a	n/a
29	POLR2A	chr6:28129278-28129829	GM10847	blood:	n/a	n/a
30	STAT5A	chr6:28129185-28129720	GM12878	blood:	n/a	chr6:28129503-28129523 chr6:28129374-28129381
31	GABPA	chr6:28129302-28129862	MCF-7	breast:	n/a	n/a
32	POU2F2	chr6:28129352-28129845	GM12891	blood:	n/a	n/a
33	CEBPD	chr6:28129205-28129741	HepG2	liver:	n/a	n/a
34	POLR2A	chr6:28129286-28129797	H1-neurons	neurons:	n/a	n/a
35	POLR2A	chr6:28129175-28129881	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr6:28129351-28129827	GM12892	blood:	n/a	n/a
37	HEY1	chr6:28129221-28129839	K562	blood:	n/a	n/a
38	SPI1	chr6:28129252-28129799	HL-60	blood:	n/a	n/a
39	HEY1	chr6:28129184-28129848	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:28128691-28129840	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr6:28129206-28129837	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:28129173-28129830	GM12891	blood:	n/a	n/a
43	POLR2A	chr6:28129342-28129833	Gliobla	brain:	n/a	n/a
44	POLR2A	chr6:28129267-28129746	Hela-S3	cervix:	n/a	n/a
45	MAX	chr6:28129425-28129717	H1-hESC	embryonic stem cell:	n/a	n/a
46	BHLHE40	chr6:28129449-28129738	K562	blood:	n/a	n/a
47	PML	chr6:28129291-28129866	K562	blood:	n/a	n/a
48	POLR2A	chr6:28129295-28129766	HepG2	liver:	n/a	n/a
49	ELK4	chr6:28129243-28129859	HEK293	kidney:	n/a	chr6:28129504-28129515 chr6:28129521-28129532 chr6:28129538-28129549
50	MAX	chr6:28129210-28129831	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28109577..28112061-chr6:28128257..28130394,3	MCF-7	breast:
2	chr17:73851685..73852659-chr6:28129475..28130353,2	Hela-S3	cervix:
3	chr6:28129539..28132293-chr6:28218155..28220468,2	K562	blood:
4	chr6:28126892..28131515-chr6:28301205..28304944,6	K562	blood:
5	chr6:27775710..27777880-chr6:28129434..28132036,2	K562	blood:
6	chr6:28127970..28130555-chr6:28316475..28318965,2	K562	blood:
7	chr6:28129397..28131360-chr6:28191862..28193480,2	K562	blood:
8	chr6:27857955..27860857-chr6:28129284..28131805,2	K562	blood:

Variant related genes	Relation type
ZNF192P1	TF binding region
ENSG00000198315	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000132471	Chromatin interaction
ENSG00000187626	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 31 )

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

rs_ID	r²[population]
rs1150668	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1150670	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150679	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150686	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150690	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1150691	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs1150694	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1150705	0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1150707	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1150709	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1150711	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs1150716	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1150724	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1150726	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs12214383	0.83[ASW][hapmap];0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
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];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	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]
rs1233713	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12530158	0.81[JPT][hapmap]
rs13408	0.83[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs149956	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs149963	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149971	0.83[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][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];0.83[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap]
rs1531681	0.83[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][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];0.92[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1736891	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1736895	0.83[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs1778484	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs1997660	0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs2021826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs213236	0.96[CEU][hapmap]
rs213237	0.96[CEU][hapmap];0.84[MEX][hapmap]
rs213238	0.96[CEU][hapmap]
rs213240	1.00[CEU][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2142730	0.96[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.83[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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2791333	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34024998	0.81[EUR][1000 genomes]
rs4713158	0.82[AMR][1000 genomes]
rs707907	0.96[MEX][hapmap];0.86[TSI][hapmap]
rs7206	0.96[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs853683	0.96[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs853684	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs853690	0.96[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs853693	0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs9301	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]
rs9468333	0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs1225618	ZSCAN31	cis	lung	GTEx
rs1225618	AL022393.7	cis	Nerve Tibial	GTEx
rs1225618	ZNF323	cis	parietal	SCAN
rs1225618	ZNF192	cis	cerebellum	SCAN
rs1225618	ZSCAN23	cis	parietal	SCAN
rs1225618	ZSCAN23	cis	cerebellum	SCAN
rs1225618	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1225618	BTN3A3	cis	parietal	SCAN
rs1225618	ZSCAN23	cis	Artery Tibial	GTEx
rs1225618	ZKSCAN3	cis	cerebellum	SCAN
rs1225618	AL022393.7	cis	Artery Aorta	GTEx
rs1225618	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs1225618	NKAPL	cis	parietal	SCAN
rs1225618	ZNF323	cis	cerebellum	SCAN
rs1225618	AL022393.7	cis	Muscle Skeletal	GTEx
rs1225618	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1225618	ZNF187	cis	cerebellum	SCAN
rs1225618	AL022393.7	cis	Artery Tibial	GTEx
rs1225618	AL022393.7	cis	lung	GTEx
rs1225618	ZKSCAN3	cis	parietal	SCAN
rs1225618	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1225618	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1225618	RP5-874C20.3	cis	Thyroid	GTEx
rs1225618	HIST1H3I	cis	cerebellum	SCAN
rs1225618	ZSCAN31	cis	Thyroid	GTEx
rs1225618	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1225618	ZNF323	cis	Temporal Cortex	GTEx
rs1225618	ZNF323	cis	Cerebellum	GTEx
rs1225618	ZSCAN23	cis	lung	GTEx
rs1225618	ZNF323	cis	Frontal Cortex	GTEx
rs1225618	ZSCAN23	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28127000-28134200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:28128800-28129800	Active TSS	Brain Germinal Matrix	brain
3	chr6:28128800-28130000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:28129000-28129800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:28129000-28129800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:28129000-28129800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:28129000-28129800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:28129000-28129800	Active TSS	NHEK	skin
9	chr6:28129000-28130000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:28129000-28130000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:28129000-28130000	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:28129000-28130000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr6:28129000-28130000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr6:28129000-28130000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:28129000-28130000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:28129000-28130000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:28129000-28130000	Active TSS	Fetal Intestine Large	intestine
18	chr6:28129000-28130000	Flanking Active TSS	Fetal Muscle Leg	muscle
19	chr6:28129000-28130000	Active TSS	A549	lung
20	chr6:28129000-28130000	Active TSS	HepG2	liver
21	chr6:28129000-28130000	Active TSS	HMEC	breast
22	chr6:28129000-28130200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr6:28129000-28130200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:28129000-28130200	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr6:28129000-28130200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr6:28129000-28130200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:28129000-28130200	Active TSS	Fetal Brain Female	brain
28	chr6:28129000-28130200	Active TSS	Fetal Kidney	kidney
29	chr6:28129000-28130200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr6:28129000-28130400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:28129000-28130400	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr6:28129000-28130400	Active TSS	Psoas Muscle	Psoas
33	chr6:28129000-28130400	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr6:28129000-28130600	Active TSS	GM12878-XiMat	blood
35	chr6:28129200-28129800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:28129200-28129800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:28129200-28129800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:28129200-28129800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:28129200-28129800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:28129200-28129800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr6:28129200-28129800	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr6:28129200-28129800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr6:28129200-28129800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:28129200-28129800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:28129200-28129800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr6:28129200-28129800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr6:28129200-28129800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:28129200-28129800	Active TSS	Muscle Satellite Cultured Cells	--
49	chr6:28129200-28129800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:28129200-28129800	Active TSS	Brain Angular Gyrus	brain

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