Variant report

Variant	rs2844663
Chromosome Location	chr6:30815951-30815952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr6:30815803-30816412	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:30815022-30816209	H1-hESC	embryonic stem cell:	n/a	n/a
3	GTF2F1	chr6:30815454-30816202	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr6:30815728-30816163	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr6:30815053-30816382	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:30815089-30816152	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP1	chr6:30815740-30816367	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:30815167-30816396	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:30815794-30816120	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF7	chr6:30815076-30816208	H1-hESC	embryonic stem cell:	n/a	n/a
11	JUND	chr6:30815409-30816569	H1-hESC	embryonic stem cell:	n/a	chr6:30815509-30815518
12	BACH1	chr6:30815890-30816338	H1-hESC	embryonic stem cell:	n/a	n/a
13	HDAC2	chr6:30815935-30816310	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr6:30815741-30816348	H1-hESC	embryonic stem cell:	n/a	n/a
15	MYC	chr6:30815131-30816646	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr6:30815294-30816221	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAFK	chr6:30815844-30816616	H1-hESC	embryonic stem cell:	n/a	n/a
18	CEBPB	chr6:30815715-30816272	H1-hESC	embryonic stem cell:	n/a	n/a
19	TAF1	chr6:30815117-30816241	H1-hESC	embryonic stem cell:	n/a	n/a
20	JUN	chr6:30815905-30816265	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr6:30815018-30816185	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOS	chr6:30815791-30815952	MCF10A-Er-Src	breast:	n/a	n/a
23	TCF12	chr6:30815828-30816311	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr6:30815118-30816224	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr6:30815674-30816248	H1-hESC	embryonic stem cell:	n/a	n/a
26	JUND	chr6:30815833-30816053	H1-hESC	embryonic stem cell:	n/a	n/a
27	TCF12	chr6:30815838-30816291	H1-hESC	embryonic stem cell:	n/a	n/a
28	SP1	chr6:30815853-30816398	H1-hESC	embryonic stem cell:	n/a	n/a
29	SIN3A	chr6:30815255-30816572	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr6:30815151-30816300	H1-hESC	embryonic stem cell:	n/a	n/a
31	EP300	chr6:30815761-30816271	H1-hESC	embryonic stem cell:	n/a	n/a
32	TEAD4	chr6:30815903-30816412	H1-hESC	embryonic stem cell:	n/a	n/a
33	FOS	chr6:30815773-30816041	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30796590..30799414-chr6:30814456..30816508,2	K562	blood:
2	chr6:30814424..30817937-chr6:30849019..30852528,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-12	chr6:30815745-30816079	NONHSAT108684

No data

Variant related genes	Relation type
ENSG00000237923	TF binding region
ENSG00000204580	Chromatin interaction
ENSG00000214894	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1264297	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264298	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264299	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264300	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264301	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264302	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264303	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264305	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1264307	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264309	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264317	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264320	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264332	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264342	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17189763	0.85[EUR][1000 genomes]
rs2074506	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240804	0.87[EUR][1000 genomes]
rs2249459	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2252760	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252856	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252863	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394856	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517449	0.89[EUR][1000 genomes]
rs2517457	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517461	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517462	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517463	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517466	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517468	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517573	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517575	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517577	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517582	0.85[EUR][1000 genomes]
rs2532920	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2532921	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2532927	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2532928	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2532929	0.81[EUR][1000 genomes]
rs2532930	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2532933	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532935	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2532936	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532937	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532938	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532939	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532940	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532942	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532943	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535325	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2535326	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2535327	0.87[EUR][1000 genomes]
rs2535329	0.87[EUR][1000 genomes]
rs2535330	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535331	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535335	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535336	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535337	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2535339	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844652	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844654	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844655	0.87[EUR][1000 genomes]
rs2844658	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844662	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844664	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844698	0.83[ASN][1000 genomes]
rs2844699	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844702	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130657	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753726	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7738138	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7756286	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs887381	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9262288	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262289	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262290	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262291	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262292	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262293	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262294	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
5	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
7	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2844663	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL
rs2844663	GRM4	cis	parietal	SCAN
rs2844663	HIST1H2AH	cis	cerebellum	SCAN
rs2844663	DDR1	cis	lymphoblastoid	seeQTL
rs2844663	LTB	cis	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30806800-30816200	Enhancers	Placenta	Placenta
2	chr6:30812000-30816200	Enhancers	Fetal Thymus	thymus
3	chr6:30812400-30817000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:30812400-30822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:30812600-30820600	Weak transcription	Right Atrium	heart
6	chr6:30812800-30817000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:30813600-30816000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:30814000-30817000	Weak transcription	Fetal Intestine Small	intestine
9	chr6:30814600-30816200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:30814800-30816200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr6:30814800-30816200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:30814800-30816200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:30814800-30816200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:30814800-30816200	Enhancers	Fetal Kidney	kidney
15	chr6:30814800-30816400	Enhancers	NHEK	skin
16	chr6:30814800-30816600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:30814800-30817600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:30815000-30816000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr6:30815000-30816200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:30815000-30816600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:30815000-30816600	Enhancers	Fetal Heart	heart
22	chr6:30815200-30816000	Enhancers	Fetal Lung	lung
23	chr6:30815200-30816000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:30815200-30816200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:30815200-30816200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:30815400-30816000	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr6:30815400-30816000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr6:30815400-30816200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:30815400-30816400	Active TSS	H1 Cell Line	embryonic stem cell
30	chr6:30815400-30816600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr6:30815800-30816000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr6:30815800-30816200	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr6:30815800-30816200	Active TSS	iPS-18 Cell Line	embryonic stem cell

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