Variant report

Variant	rs3088063
Chromosome Location	chr19:35838076-35838077
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	USF2	chr19:35837485-35839010	GM12878	blood:	n/a	n/a
2	NFIC	chr19:35837299-35838965	GM12878	blood:	n/a	n/a
3	CUX1	chr19:35837331-35839042	GM12878	blood:	n/a	n/a
4	BHLHE40	chr19:35836713-35839191	GM12878	blood:	n/a	n/a
5	ATF2	chr19:35837247-35839038	GM12878	blood:	n/a	n/a
6	FOXM1	chr19:35837220-35839303	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:35834081-35844229	GM12878	blood:	n/a	n/a
8	POU2F2	chr19:35837429-35838951	GM12878	blood:	n/a	chr19:35838670-35838677 chr19:35838668-35838678 chr19:35838666-35838681 chr19:35838665-35838683 chr19:35838667-35838681 chr19:35838667-35838679 chr19:35838668-35838678 chr19:35838669-35838678
9	POLR2A	chr19:35836311-35839226	GM12878	blood:	n/a	n/a
10	CHD1	chr19:35837266-35839139	GM12878	blood:	n/a	n/a
11	ATF2	chr19:35837301-35839275	GM12878	blood:	n/a	n/a
12	YY1	chr19:35838068-35838887	GM12892	blood:	n/a	n/a
13	BCL3	chr19:35837388-35839100	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:35836562-35839254	GM18951	blood:	n/a	n/a
15	POLR2A	chr19:35836286-35839245	GM12892	blood:	n/a	n/a
16	POLR2A	chr19:35836339-35843943	GM19193	blood:	n/a	n/a
17	EP300	chr19:35836855-35839120	GM12878	blood:	n/a	n/a
18	EP300	chr19:35837269-35838959	GM12878	blood:	n/a	n/a
19	PML	chr19:35836159-35841607	GM12878	blood:	n/a	n/a
20	CREB1	chr19:35837266-35839064	GM12878	blood:	n/a	n/a
21	MTA3	chr19:35837234-35839313	GM12878	blood:	n/a	n/a
22	BCLAF1	chr19:35836768-35839223	GM12878	blood:	n/a	chr19:35839148-35839157
23	RELA	chr19:35836740-35839176	GM18951	blood:	n/a	n/a
24	RELA	chr19:35836498-35839120	GM18505	blood:	n/a	n/a
25	POLR2A	chr19:35836392-35841540	GM12878	blood:	n/a	n/a
26	RELA	chr19:35837316-35839118	GM19099	blood:	n/a	n/a
27	PML	chr19:35838060-35838838	GM12878	blood:	n/a	n/a
28	YY1	chr19:35838030-35838849	GM12891	blood:	n/a	n/a
29	POU2F2	chr19:35837416-35839185	GM12891	blood:	n/a	chr19:35838670-35838677 chr19:35838668-35838678 chr19:35838666-35838681 chr19:35838665-35838683 chr19:35838667-35838681 chr19:35838667-35838679 chr19:35838668-35838678 chr19:35838669-35838678
30	YY1	chr19:35837352-35838961	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:35838016-35839051	GM12891	blood:	n/a	n/a
32	MAX	chr19:35836738-35839173	GM12878	blood:	n/a	chr19:35839015-35839022 chr19:35839014-35839023 chr19:35839014-35839023
33	NFIC	chr19:35836758-35839422	GM12878	blood:	n/a	n/a
34	NFATC1	chr19:35836440-35841654	GM12878	blood:	n/a	n/a
35	ZNF143	chr19:35837482-35838082	GM12878	blood:	n/a	n/a
36	MTA3	chr19:35836288-35841818	GM12878	blood:	n/a	n/a
37	NRF1	chr19:35837481-35838175	GM12878	blood:	n/a	n/a
38	RELA	chr19:35837410-35839060	GM10847	blood:	n/a	n/a
39	EBF1	chr19:35837255-35839017	GM12878	blood:	n/a	n/a
40	RUNX3	chr19:35836555-35839349	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:35834959-35844013	GM12892	blood:	n/a	n/a
42	MXI1	chr19:35837288-35838920	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:35836351-35841707	GM12891	blood:	n/a	n/a
44	TBL1XR1	chr19:35837296-35838966	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:35836400-35842018	GM12892	blood:	n/a	n/a
46	CEBPB	chr19:35837374-35839176	GM12878	blood:	n/a	chr19:35838744-35838755 chr19:35838744-35838757
47	STAT1	chr19:35837286-35838808	GM12878	blood:	n/a	n/a
48	MAZ	chr19:35836910-35839151	GM12878	blood:	n/a	chr19:35839015-35839022 chr19:35839014-35839023 chr19:35839014-35839023
49	RUNX3	chr19:35836645-35839351	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:35836358-35841827	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:35759183..35761582-chr19:35836760..35840257,3	MCF-7	breast:
2	chr19:35837012..35839854-chr19:35847612..35849842,2	MCF-7	breast:

Variant related genes	Relation type
FFAR1	TF binding region
ENSG00000185897	Chromatin interaction
ENSG00000105698	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10406829	1.00[MEX][hapmap]
rs10423648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10426830	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16970196	1.00[MEX][hapmap]
rs16970204	1.00[MEX][hapmap]
rs16970264	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58174206	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247137	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8108571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
8	esv1828194	chr19:35812566-35865695	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067129	chr19:35827036-35849310	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv173	chr19:35837405-35866835	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2471	chr19:35837405-35903115	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35817600-35844000	Weak transcription	Brain Angular Gyrus	brain
2	chr19:35825400-35838200	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr19:35825400-35838200	Strong transcription	Ovary	ovary
4	chr19:35828400-35838200	Strong transcription	Brain Hippocampus Middle	brain
5	chr19:35832800-35838800	Strong transcription	Brain Inferior Temporal Lobe	brain
6	chr19:35835600-35839800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:35835800-35840000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:35836400-35838200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr19:35836400-35838200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
10	chr19:35836400-35840400	Enhancers	Primary hematopoietic stem cells	blood
11	chr19:35836600-35838600	Enhancers	K562	blood
12	chr19:35836600-35839000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr19:35836600-35839000	Bivalent Enhancer	Placenta	Placenta
14	chr19:35836600-35839200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr19:35836600-35839800	Enhancers	Fetal Thymus	thymus
16	chr19:35836800-35838800	Enhancers	HepG2	liver
17	chr19:35836800-35839200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:35836800-35839200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr19:35836800-35843800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:35836800-35848000	Weak transcription	Brain Substantia Nigra	brain
21	chr19:35837000-35838200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr19:35837000-35839200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:35837000-35839200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:35837000-35839200	Enhancers	Duodenum Mucosa	Duodenum
25	chr19:35837400-35838200	Enhancers	Colonic Mucosa	Colon
26	chr19:35837400-35838200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr19:35837400-35839200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:35837400-35839200	Bivalent Enhancer	Dnd41	blood
29	chr19:35837400-35839400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr19:35837400-35840800	Enhancers	Spleen	Spleen
31	chr19:35837600-35838200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:35837600-35838200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr19:35837600-35838400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr19:35837600-35838600	Enhancers	Lung	lung
35	chr19:35837600-35838600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr19:35837600-35843600	Weak transcription	Brain Anterior Caudate	brain
37	chr19:35837800-35838600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:35837800-35838600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:35837800-35838600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:35837800-35838800	Enhancers	Thymus	Thymus
41	chr19:35837800-35839000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr19:35838000-35838200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr19:35838000-35838200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr19:35838000-35838200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr19:35838000-35838400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr19:35838000-35838400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
47	chr19:35838000-35838600	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr19:35838000-35838800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:35838000-35839000	Flanking Active TSS	Primary B cells from cord blood	blood

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