Variant report

Variant	rs7100
Chromosome Location	chr3:49053219-49053220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49052944-49056404	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:49051467-49053491	K562	blood:	n/a	n/a
3	POLR2A	chr3:49053099-49053374	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:49050113-49067296	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:49053148-49056378	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:49052840-49053300	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:49052980-49056417	HL-60	blood:	n/a	n/a
8	POLR2A	chr3:49051503-49056616	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr3:49052474-49059791	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr3:49052978-49053954	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:49049681-49055610	GM12891	blood:	n/a	n/a
12	POLR2A	chr3:49048502-49056486	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:49048842-49056486	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:49048845-49056419	GM12891	blood:	n/a	n/a
15	POLR2A	chr3:49052548-49056350	K562	blood:	n/a	n/a
16	POLR2A	chr3:49051566-49056520	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:49053216-49054717	NB4	blood:	n/a	n/a
18	POLR2A	chr3:49051954-49056421	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:49051952-49055393	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:49052566-49055998	A549	lung:	n/a	n/a
21	POLR2A	chr3:49053041-49054590	GM12891	blood:	n/a	n/a
22	POLR2A	chr3:49052732-49053482	U87	brain:	n/a	n/a
23	POLR2A	chr3:49050908-49056374	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr3:49052097-49056367	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr3:49052736-49056323	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr3:49048918-49055399	GM12892	blood:	n/a	n/a
27	POLR2A	chr3:49051928-49054134	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:49053083-49054397	K562	blood:	n/a	n/a
29	POLR2A	chr3:49048783-49056505	GM12892	blood:	n/a	n/a
30	POLR2A	chr3:49052798-49054881	SK-N-SH	brain:	n/a	n/a
31	MTA3	chr3:49053209-49056613	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:49048897-49056290	GM12891	blood:	n/a	n/a
33	POLR2A	chr3:49051541-49056898	K562	blood:	n/a	n/a
34	POLR2A	chr3:49053209-49056861	GM12891	blood:	n/a	n/a
35	POLR2A	chr3:49052889-49056613	HCT-116	colon:	n/a	n/a
36	POLR2A	chr3:49052846-49056620	K562	blood:	n/a	n/a
37	PML	chr3:49052717-49056611	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:49052988-49056596	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr3:49052283-49056597	HL-60	blood:	n/a	n/a
40	POLR2A	chr3:49052951-49056321	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:49053095-49054648	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr3:49052322-49056514	U87	brain:	n/a	n/a
43	POLR2A	chr3:49052952-49056301	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:49052939-49056105	HepG2	liver:	n/a	n/a
45	POLR2A	chr3:49053008-49053294	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr3:49050568-49056569	SK-N-MC	brain:	n/a	n/a
47	POLR2A	chr3:49048769-49067292	GM12892	blood:	n/a	n/a
48	POLR2A	chr3:49052996-49053329	HepG2	liver:	n/a	n/a
49	SP1	chr3:49052696-49053387	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:49051911-49056797	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49053208-49053258	HRCEpiC	kidney:	n/a
2	chr3:49053208-49053258	GM12892	blood:	n/a
3	chr3:49053208-49053258	K562	blood:	n/a
4	chr3:49053208-49053258	GM19239	blood:	n/a
5	chr3:49053208-49053258	HNPCEpiC	eye:	n/a
6	chr3:49053208-49053258	AoSMC	blood vessel:	n/a
7	chr3:49053208-49053258	HEEpiC	esophagus:	n/a
8	chr3:49053208-49053258	GM12878	blood:	n/a
9	chr3:49053208-49053258	HEK293	kidney:	embryo
10	chr3:49053208-49053258	H1-hESC	embryonic stem cell:	embryo
11	chr3:49053208-49053258	IMR90	lung:	fetal
12	chr3:49053208-49053258	GM12891	blood:	n/a
13	chr3:49053208-49053258	MCF-7	breast:	n/a
14	chr3:49053208-49053258	PrEC	prostate:	n/a
15	chr3:49053208-49053258	SKMC	muscle:	n/a
16	chr3:49053208-49053258	SK-N-SH	brain:	n/a
17	chr3:49053208-49053258	HIPEpiC	eye:	n/a
18	chr3:49053208-49053258	AG09309	skin:	n/a
19	chr3:49053208-49053258	HPAEpiC	pulmonary alveolar:	n/a
20	chr3:49053208-49053258	AG10803	skin:	n/a
21	chr3:49053208-49053258	HRE	kidney:	n/a
22	chr3:49053208-49053258	HRPEpiC	eye:	n/a
23	chr3:49053208-49053258	LNCaP	prostate:	n/a
24	chr3:49053208-49053258	PANC-1	pancreas:	n/a
25	chr3:49053208-49053258	NB4	blood:	n/a
26	chr3:49053208-49053258	ovcar-3	ovarian:	n/a
27	chr3:49053208-49053258	HepG2	liver:	n/a
28	chr3:49053208-49053258	HL-60	blood:	n/a
29	chr3:49053208-49053258	HCPEpiC	choroid plexus:	n/a
30	chr3:49053208-49053258	SK-N-MC	brain:	n/a
31	chr3:49053208-49053258	U87	brain:	n/a
32	chr3:49053208-49053258	SK-N-SH_RA	brain:	n/a
33	chr3:49053208-49053258	HCM	heart:	n/a
34	chr3:49053208-49053258	HCF	heart:	n/a
35	chr3:49053208-49053258	NH-A	brain:	n/a
36	chr3:49053208-49053258	AG04449	skin:	fetal
37	chr3:49053208-49053258	MCF10A-Er-Src	breast:	n/a
38	chr3:49053208-49053258	Hepatocyte	liver:	n/a
39	chr3:49053208-49053258	HUVEC	blood vessel:	n/a
40	chr3:49053208-49053258	SAEC	small airway:	n/a
41	chr3:49053208-49053258	RPTEC	kidney:	n/a
42	chr3:49053208-49053258	GM06990	blood:	n/a
43	chr3:49053208-49053258	Caco-2	colon:	n/a
44	chr3:49053208-49053258	HMEC	breast:	n/a
45	chr3:49053208-49053258	Hela-S3	cervix:	n/a
46	chr3:49053208-49053258	ECC-1	luminal epithelium:	n/a
47	chr3:49053208-49053258	PFSK-1	brain:	n/a
48	chr3:49053208-49053258	BE2_C	brain:	n/a
49	chr3:49053208-49053258	NHBE	bronchial:	n/a
50	chr3:49053208-49053258	ProgFib	skin:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49052737..49055601-chr3:49169653..49171785,2	MCF-7	breast:
2	chr3:49051266..49053543-chr3:49156986..49159696,2	MCF-7	breast:
3	chr3:49052218..49068794-chr3:49126865..49133927,44	K562	blood:
4	chr3:49050440..49054790-chr3:49130798..49133846,4	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFAF3	TF binding region
NDUFAF3	CpG island
ENSG00000198218	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000172046	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11130181	0.86[EUR][1000 genomes]
rs11707968	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12715430	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13084037	1.00[YRI][hapmap]
rs13099075	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3087866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[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]
rs4292260	0.86[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs4955411	0.86[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs4955416	0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4955426	0.86[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs4955439	0.82[MEX][hapmap]
rs4974081	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4974083	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4974088	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs62259536	0.81[EUR][1000 genomes]
rs6414614	0.93[EUR][1000 genomes]
rs6446200	0.88[EUR][1000 genomes]
rs6446204	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6446247	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6772452	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6787808	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs6798112	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7372883	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7373072	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs7429661	0.82[MEX][hapmap]
rs7434187	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621226	0.89[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7621347	0.86[EUR][1000 genomes]
rs7653408	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9284885	0.91[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs9810318	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9864243	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9865051	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases

mRNA abundance (count:34)

SNP	Gene	Cis/trans	Tissue	Source
rs7100	WDR6	cis	cerebellum	SCAN
rs7100	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7100	AMT	cis	lung	GTEx
rs7100	AMT	cis	Whole Blood	GTEx
rs7100	GPX1	cis	parietal	SCAN
rs7100	P4HTM	cis	lung	GTEx
rs7100	DALRD3	cis	parietal	SCAN
rs7100	PHF7	cis	parietal	SCAN
rs7100	AMT	cis	Nerve Tibial	GTEx
rs7100	ARIH2	cis	Thyroid	GTEx
rs7100	AMT	cis	Artery Aorta	GTEx
rs7100	NICN1	cis	cerebellum	SCAN
rs7100	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7100	DALRD3	cis	cerebellum	SCAN
rs7100	NICN1	cis	Thyroid	GTEx
rs7100	AMT	cis	Artery Tibial	GTEx
rs7100	WDR6	cis	Heart Left Ventricle	GTEx
rs7100	LZTFL1	cis	cerebellum	SCAN
rs7100	AMT	cis	Thyroid	GTEx
rs7100	AMT	cis	Adipose Subcutaneous	GTEx
rs7100	NICN1-AS1	cis	Thyroid	GTEx
rs7100	TLR9	cis	parietal	SCAN
rs7100	P4HTM	cis	parietal	SCAN
rs7100	AMT	cis	parietal	SCAN
rs7100	WDR6	cis	Nerve Tibial	GTEx
rs7100	NICN1	cis	parietal	SCAN
rs7100	AMT	cis	cerebellum	SCAN
rs7100	NCKIPSD	cis	Nerve Tibial	GTEx
rs7100	NCKIPSD	cis	parietal	SCAN
rs7100	WDR6	cis	parietal	SCAN
rs7100	WDR6	cis	Muscle Skeletal	GTEx
rs7100	IQCF1	cis	cerebellum	SCAN
rs7100	QRICH1	cis	cerebellum	SCAN
rs7100	ZNF589	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49045800-49055000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49046200-49054400	Strong transcription	Fetal Stomach	stomach
3	chr3:49046200-49054600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:49046200-49054600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:49046200-49054800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:49046400-49054200	Strong transcription	Fetal Intestine Small	intestine
7	chr3:49046600-49054200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:49046800-49054200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:49046800-49054400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:49047000-49054200	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:49047600-49054800	Strong transcription	Lung	lung
12	chr3:49048400-49054400	Strong transcription	Fetal Intestine Large	intestine
13	chr3:49048400-49054600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:49048600-49053400	Strong transcription	Primary hematopoietic stem cells	blood
15	chr3:49048600-49054400	Strong transcription	Thymus	Thymus
16	chr3:49048800-49053800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:49048800-49053800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:49048800-49053800	Strong transcription	Fetal Thymus	thymus
19	chr3:49048800-49054000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:49048800-49054000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:49048800-49054000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:49048800-49054000	Strong transcription	Primary B cells from cord blood	blood
23	chr3:49048800-49054000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr3:49048800-49054200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr3:49048800-49054200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:49048800-49054200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:49048800-49054200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:49048800-49054200	Strong transcription	Primary T cells from cord blood	blood
29	chr3:49048800-49054200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:49048800-49054200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:49048800-49054400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:49048800-49054400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:49048800-49054400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:49048800-49054400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:49048800-49054600	Strong transcription	Fetal Brain Female	brain
36	chr3:49048800-49054600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr3:49048800-49054800	Strong transcription	Brain Cingulate Gyrus	brain
38	chr3:49049000-49053600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:49049000-49053800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr3:49049000-49053800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:49049000-49054000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:49049000-49054000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:49049000-49054000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:49049000-49054200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:49049000-49054200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:49049000-49054200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:49049000-49054200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:49049000-49054200	Strong transcription	A549	lung
49	chr3:49049000-49054400	Strong transcription	Adipose Nuclei	Adipose
50	chr3:49049000-49054400	Strong transcription	Liver	Liver

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