Variant report

Variant	rs13321674
Chromosome Location	chr3:51704721-51704722
allele	C/T
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	EP300	chr3:51704694-51705112	T-47D	breast:	n/a	n/a
2	POLR2A	chr3:51704684-51706405	GM18505	blood:	n/a	n/a
3	POLR2A	chr3:51704671-51706350	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:51704696-51704914	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:51704628-51706205	GM12892	blood:	n/a	n/a
6	MXI1	chr3:51704446-51706405	SK-N-SH	brain:	n/a	chr3:51705117-51705132 chr3:51705119-51705134
7	CTCF	chr3:51704640-51704790	GM12874	blood:	n/a	n/a
8	NFATC1	chr3:51704608-51705417	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:51704095-51706320	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr3:51704680-51704830	HMEC	breast:	n/a	n/a
11	TFAP2C	chr3:51704624-51706156	Hela-S3	cervix:	n/a	n/a
12	ZNF263	chr3:51704459-51706162	HEK293-T-REx	kidney:	n/a	chr3:51704522-51704531
13	CTCF	chr3:51704580-51704730	AG10803	skin:	n/a	n/a
14	POLR2A	chr3:51704521-51706303	K562	blood:	n/a	n/a
15	CTCF	chr3:51704580-51704730	SK-N-SH_RA	brain:	n/a	n/a
16	MYC	chr3:51704483-51706154	MCF10A-Er-Src	breast:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
17	SMARCC1	chr3:51704664-51706319	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr3:51704644-51705164	HepG2	liver:	n/a	n/a
19	E2F4	chr3:51704570-51705404	MCF10A-Er-Src	breast:	n/a	chr3:51705167-51705176 chr3:51705058-51705070
20	POLR2A	chr3:51704348-51706208	MCF10A-Er-Src	breast:	n/a	n/a
21	BRCA1	chr3:51704714-51704918	GM12878	blood:	n/a	n/a
22	MXI1	chr3:51704715-51706249	Hela-S3	cervix:	n/a	chr3:51705117-51705132 chr3:51705119-51705134
23	POLR2A	chr3:51704373-51706469	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:51704251-51706245	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:51704685-51706349	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr3:51704660-51704810	HPF	lung:	n/a	n/a
27	ELF1	chr3:51704656-51706374	GM12878	blood:	n/a	chr3:51705524-51705536 chr3:51705147-51705159 chr3:51705853-51705862
28	MAZ	chr3:51704549-51706313	IMR90	lung:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
29	MTA3	chr3:51704299-51706382	GM12878	blood:	n/a	n/a
30	TFAP2A	chr3:51704671-51706103	Hela-S3	cervix:	n/a	chr3:51705547-51705555 chr3:51705546-51705557 chr3:51705547-51705555 chr3:51705548-51705556 chr3:51705547-51705555 chr3:51705548-51705556 chr3:51705546-51705557 chr3:51705546-51705557 chr3:51705548-51705556
31	POLR2A	chr3:51704375-51706806	GM12891	blood:	n/a	n/a
32	CEBPB	chr3:51704644-51705335	Hela-S3	cervix:	n/a	n/a
33	MXI1	chr3:51703826-51706344	IMR90	lung:	n/a	chr3:51705117-51705132 chr3:51705119-51705134
34	HCFC1	chr3:51704425-51706373	Hela-S3	cervix:	n/a	n/a
35	PML	chr3:51704551-51706378	GM12878	blood:	n/a	n/a
36	SMARCB1	chr3:51704529-51706286	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr3:51704672-51706709	SK-N-MC	brain:	n/a	n/a
38	STAT5A	chr3:51704370-51706159	GM12878	blood:	n/a	chr3:51704671-51704683 chr3:51704687-51704695 chr3:51704920-51704932
39	POLR2A	chr3:51704720-51706360	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51532457..51535099-chr3:51703667..51706623,4	MCF-7	breast:
2	chr3:51532560..51534895-chr3:51704003..51706915,3	K562	blood:
3	chr3:51703488..51706346-chr3:51714334..51716919,2	MCF-7	breast:
4	chr3:51533144..51535964-chr3:51704671..51707377,2	MCF-7	breast:
5	chr3:51704425..51707228-chr3:51714036..51717789,3	MCF-7	breast:
6	chr3:51704201..51711015-chr3:51712254..51717093,7	K562	blood:
7	chr3:51532096..51536424-chr3:51702408..51707498,7	K562	blood:
8	chr3:51702918..51706936-chr3:51707889..51711767,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IQCF6-2	chr3:51704665-51704909	NONHSAT089874

Variant related genes	Relation type
TEX264	TF binding region
ENSG00000145041	Chromatin interaction
ENSG00000164081	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs12330534	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13314120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13325153	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[YRI][hapmap]
rs13327225	1.00[MEX][hapmap]
rs13433729	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051799	1.00[AMR][1000 genomes]
rs17051832	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421789	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28452990	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	1.00[AMR][1000 genomes]
rs28653367	1.00[AMR][1000 genomes]
rs2883900	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549265	1.00[AMR][1000 genomes]
rs56942057	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6792143	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs6806124	1.00[MEX][hapmap]
rs72951441	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9808940	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9809757	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815475	1.00[MEX][hapmap]
rs9815684	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	1.00[AMR][1000 genomes]
rs9827917	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838294	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839516	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840331	1.00[AMR][1000 genomes]
rs9842066	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855809	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857893	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858497	1.00[AMR][1000 genomes]
rs9864213	1.00[AMR][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878564	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9880050	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880909	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	1.00[AMR][1000 genomes]
rs9882601	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv965167	chr3:51702892-51707059	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1814919	chr3:51703488-51752684	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51694200-51704800	Weak transcription	Psoas Muscle	Psoas
2	chr3:51697400-51704800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:51697400-51704800	Weak transcription	Aorta	Aorta
4	chr3:51698000-51704800	Weak transcription	Ovary	ovary
5	chr3:51702800-51704800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:51702800-51704800	Enhancers	Placenta	Placenta
7	chr3:51703000-51704800	Enhancers	Fetal Muscle Leg	muscle
8	chr3:51703000-51704800	Enhancers	Pancreas	Pancrea
9	chr3:51703000-51704800	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr3:51703000-51707800	Enhancers	Fetal Heart	heart
11	chr3:51703200-51704800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:51703200-51704800	Genic enhancers	NHLF	lung
13	chr3:51703400-51704800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:51703400-51704800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:51703400-51704800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:51703400-51704800	Enhancers	Spleen	Spleen
17	chr3:51703600-51704800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:51703600-51704800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:51703600-51704800	Enhancers	Gastric	stomach
20	chr3:51703600-51705200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr3:51703800-51704800	Enhancers	Lung	lung
22	chr3:51704000-51705000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:51704000-51705000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr3:51704000-51705000	Flanking Active TSS	Hela-S3	cervix
25	chr3:51704000-51705200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr3:51704000-51705600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:51704200-51705000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:51704200-51705000	Enhancers	Small Intestine	intestine
29	chr3:51704200-51705000	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr3:51704200-51705000	Flanking Active TSS	HepG2	liver
31	chr3:51704200-51705200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr3:51704400-51704800	Enhancers	Fetal Intestine Large	intestine
33	chr3:51704400-51704800	Enhancers	HUVEC	blood vessel
34	chr3:51704400-51705000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr3:51704400-51705000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr3:51704400-51705000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr3:51704400-51705000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr3:51704400-51705000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr3:51704400-51705000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr3:51704400-51705000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:51704400-51705000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr3:51704400-51705000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:51704400-51705000	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr3:51704400-51705000	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr3:51704400-51705000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:51704400-51705000	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr3:51704400-51705000	Flanking Active TSS	Fetal Brain Male	brain
48	chr3:51704400-51705000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr3:51704400-51705000	Flanking Active TSS	Thymus	Thymus
50	chr3:51704400-51705000	Flanking Active TSS	GM12878-XiMat	blood

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