Variant report

Variant	rs673147
Chromosome Location	chr11:65060427-65060428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr11:65058895-65060766	IMR90	lung:	n/a	chr11:65059398-65059407 chr11:65060252-65060263 chr11:65060417-65060426
2	POLR2A	chr11:65059615-65060644	SK-N-MC	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:65060386-65060436	HCF	heart:	n/a
2	chr11:65060386-65060436	HAEpiC	amniotic membrane:	n/a
3	chr11:65060386-65060436	ECC-1	luminal epithelium:	n/a
4	chr11:65060386-65060436	HPAEpiC	pulmonary alveolar:	n/a
5	chr11:65060386-65060436	HEK293	kidney:	embryo
6	chr11:65060386-65060436	Jurkat	blood:	n/a
7	chr11:65060386-65060436	SKMC	muscle:	n/a
8	chr11:65060386-65060436	A549	lung:	n/a
9	chr11:65060386-65060436	AG04449	skin:	fetal
10	chr11:65060386-65060436	NHBE	bronchial:	n/a
11	chr11:65060386-65060436	IMR90	lung:	fetal
12	chr11:65060386-65060436	SK-N-SH	brain:	n/a
13	chr11:65060386-65060436	MCF-7	breast:	n/a
14	chr11:65060386-65060436	U87	brain:	n/a
15	chr11:65060386-65060436	HCPEpiC	choroid plexus:	n/a
16	chr11:65060386-65060436	AoSMC	blood vessel:	n/a
17	chr11:65060386-65060436	HRCEpiC	kidney:	n/a
18	chr11:65060386-65060436	Hepatocyte	liver:	n/a
19	chr11:65060386-65060436	CMK	blood:	n/a
20	chr11:65060386-65060436	ovcar-3	ovarian:	n/a
21	chr11:65060386-65060436	GM12878	blood:	n/a
22	chr11:65060386-65060436	GM12892	blood:	n/a
23	chr11:65060386-65060436	BJ	skin:	n/a
24	chr11:65060386-65060436	HepG2	liver:	n/a
25	chr11:65060386-65060436	H1-hESC	embryonic stem cell:	embryo
26	chr11:65060386-65060436	HRE	kidney:	n/a
27	chr11:65060386-65060436	RPTEC	kidney:	n/a
28	chr11:65060386-65060436	LNCaP	prostate:	n/a
29	chr11:65060386-65060436	NB4	blood:	n/a
30	chr11:65060386-65060436	HL-60	blood:	n/a
31	chr11:65060386-65060436	NT2-D1	testis:	n/a
32	chr11:65060386-65060436	PFSK-1	brain:	n/a
33	chr11:65060386-65060436	HMEC	breast:	n/a
34	chr11:65060386-65060436	ProgFib	skin:	n/a
35	chr11:65060386-65060436	Caco-2	colon:	n/a
36	chr11:65060386-65060436	K562	blood:	n/a
37	chr11:65060386-65060436	NH-A	brain:	n/a
38	chr11:65060386-65060436	HEEpiC	esophagus:	n/a
39	chr11:65060386-65060436	AG09309	skin:	n/a
40	chr11:65060386-65060436	MCF10A-Er-Src	breast:	n/a
41	chr11:65060386-65060436	PrEC	prostate:	n/a
42	chr11:65060386-65060436	HIPEpiC	eye:	n/a
43	chr11:65060386-65060436	SAEC	small airway:	n/a
44	chr11:65060386-65060436	AG04450	lung:	fetal
45	chr11:65060386-65060436	HUVEC	blood vessel:	n/a
46	chr11:65060386-65060436	GM12891	blood:	n/a
47	chr11:65060386-65060436	AG09319	gingival:	n/a
48	chr11:65060386-65060436	BE2_C	brain:	n/a
49	chr11:65060386-65060436	SK-N-MC	brain:	n/a
50	chr11:65060386-65060436	SK-N-SH_RA	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr11:65055007..65056985-chr11:65059907..65061766,3	K562	blood:
2	chr11:65057209..65061295-chr11:65190411..65193385,3	K562	blood:
3	chr11:65039605..65041396-chr11:65058643..65061112,2	K562	blood:
4	chr11:65058175..65060468-chr11:65184473..65187449,2	MCF-7	breast:
5	chr11:65060136..65062858-chr11:65077231..65083212,5	K562	blood:
6	chr11:65054454..65057317-chr11:65058868..65061656,2	MCF-7	breast:
7	chr11:65058707..65061317-chr11:65062502..65064262,2	K562	blood:
8	chr11:65058796..65060514-chr11:65089215..65091346,2	MCF-7	breast:

No data

Variant related genes	Relation type
POLA2	TF binding region
POLA2	CpG island
ENSG00000014138	Chromatin interaction
ENSG00000149798	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1152611	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1195733	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12269727	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1633466	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1783486	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes]
rs1858783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239261	0.80[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs2904966	1.00[CHB][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs2904967	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs2904979	0.80[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs2904980	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2904981	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs2904982	1.00[CHB][hapmap]
rs2904984	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2904986	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3015997	0.80[CEU][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs3015999	0.82[ASN][1000 genomes]
rs3016000	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3016001	0.82[EUR][1000 genomes]
rs3741386	1.00[CHB][hapmap]
rs4149813	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487568	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487989	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488289	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499027	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs503277	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs506280	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs507005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs509303	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs526502	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs542142	0.83[ASN][1000 genomes]
rs551523	1.00[CHB][hapmap]
rs554122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs560097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571128	0.84[EUR][1000 genomes]
rs592050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs603286	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs611910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620427	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap]
rs625427	0.83[EUR][1000 genomes]
rs626555	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs630055	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs636928	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs655433	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs667341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs668735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676114	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs676573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7116674	0.89[CHD][hapmap]
rs8638	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs673147	POLA2	cis	lymphoblastoid	seeQTL
rs673147	BATF2	cis	cerebellum	SCAN
rs673147	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs673147	POLA2	cis	parietal	SCAN
rs673147	GAL3ST3	cis	cerebellum	SCAN
rs673147	RPS6KB2	cis	cerebellum	SCAN
rs673147	PLCB3	cis	cerebellum	SCAN
rs673147	POLA2	cis	cerebellum	SCAN
rs673147	POLA2	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65031200-65064800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:65042400-65068800	Strong transcription	Fetal Thymus	thymus
3	chr11:65042800-65065000	Strong transcription	Primary T cells from cord blood	blood
4	chr11:65042800-65072800	Strong transcription	Dnd41	blood
5	chr11:65043000-65066200	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr11:65043000-65067600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:65043200-65066400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:65043200-65066600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:65043400-65067200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr11:65043400-65067200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:65043600-65065000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:65044000-65065600	Strong transcription	Thymus	Thymus
13	chr11:65044400-65066200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:65045000-65066600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr11:65045600-65065200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:65045800-65067200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:65046000-65067000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:65047600-65064800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:65047800-65075800	Weak transcription	Small Intestine	intestine
20	chr11:65048400-65065000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr11:65048400-65069000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:65050200-65061800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr11:65050200-65062200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr11:65052400-65066600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:65053200-65066200	Strong transcription	HMEC	breast
26	chr11:65053200-65067000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:65053600-65066400	Strong transcription	NHEK	skin
28	chr11:65054200-65063800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:65054200-65065000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:65054200-65065000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr11:65054600-65066000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr11:65056000-65068800	Genic enhancers	Fetal Stomach	stomach
33	chr11:65056400-65061000	Enhancers	Left Ventricle	heart
34	chr11:65056400-65062000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:65057200-65061200	Enhancers	Fetal Muscle Trunk	muscle
36	chr11:65057200-65065600	Weak transcription	Aorta	Aorta
37	chr11:65057400-65065400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:65057400-65065400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:65057600-65060800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:65057600-65061600	Enhancers	Ovary	ovary
41	chr11:65057800-65060800	Genic enhancers	Primary hematopoietic stem cells	blood
42	chr11:65057800-65061000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr11:65057800-65061400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr11:65058000-65060600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr11:65058000-65061200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr11:65058200-65060600	Enhancers	Stomach Mucosa	stomach
47	chr11:65058200-65061400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:65058400-65060600	Enhancers	Placenta Amnion	Placenta Amnion
49	chr11:65058400-65062200	Enhancers	Right Atrium	heart
50	chr11:65058600-65061000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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