Variant report

Variant	rs2442683
Chromosome Location	chr11:107729615-107729616
allele	A/C
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	ZNF384	chr11:107729482-107731027	GM12878	blood:	n/a	n/a
2	POU2F2	chr11:107729162-107729853	GM12878	blood:	n/a	n/a
3	MAZ	chr11:107728624-107730050	Hela-S3	cervix:	n/a	chr11:107729315-107729322 chr11:107729341-107729350 chr11:107729314-107729323
4	EP300	chr11:107729410-107730044	GM12878	blood:	n/a	n/a
5	KAP1	chr11:107729096-107730128	U2OS	brain:	n/a	n/a
6	MXI1	chr11:107729173-107730066	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr11:107729079-107729918	K562	blood:	n/a	n/a
8	CTCF	chr11:107729527-107729634	GM12892	blood:	n/a	n/a
9	TAF1	chr11:107729362-107729744	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr11:107728600-107730100	Hela-S3	cervix:	n/a	n/a
11	RUNX3	chr11:107728498-107730062	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:107729376-107729645	A549	lung:	n/a	n/a
13	POLR2A	chr11:107728765-107730705	GM18951	blood:	n/a	n/a
14	ELF1	chr11:107728604-107729814	GM12878	blood:	n/a	chr11:107729325-107729337 chr11:107729538-107729551
15	POLR2A	chr11:107728320-107731018	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:107729138-107729655	A549	lung:	n/a	n/a
17	SIN3AK20	chr11:107729126-107729636	K562	blood:	n/a	n/a
18	STAT3	chr11:107729440-107730111	MCF10A-Er-Src	breast:	n/a	n/a
19	MAX	chr11:107728687-107730123	A549	lung:	n/a	chr11:107729315-107729322 chr11:107729341-107729350 chr11:107729314-107729323
20	MAX	chr11:107728519-107730031	Hela-S3	cervix:	n/a	chr11:107729315-107729322 chr11:107729341-107729350 chr11:107729314-107729323
21	MYC	chr11:107728761-107730043	NB4	blood:	n/a	chr11:107729315-107729322 chr11:107729341-107729350 chr11:107729314-107729323
22	KAP1	chr11:107729044-107730757	HEK293	kidney:	n/a	n/a
23	RAD21	chr11:107728915-107730266	H1-hESC	embryonic stem cell:	n/a	chr11:107728996-107729010
24	EBF1	chr11:107729349-107729951	GM12878	blood:	n/a	n/a
25	CHD2	chr11:107728988-107730040	Hela-S3	cervix:	n/a	n/a
26	CEBPB	chr11:107728286-107730180	Hela-S3	cervix:	n/a	n/a
27	YY1	chr11:107729117-107729961	ECC-1	luminal epithelium:	n/a	chr11:107729325-107729339 chr11:107729330-107729341
28	TAF1	chr11:107728790-107730130	ECC-1	luminal epithelium:	n/a	n/a
29	ZNF143	chr11:107729075-107730018	H1-hESC	embryonic stem cell:	n/a	n/a
30	TAF1	chr11:107729187-107729758	GM12892	blood:	n/a	n/a
31	TEAD4	chr11:107729112-107729808	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr11:107729118-107729870	GM12892	blood:	n/a	n/a
33	GABPA	chr11:107729383-107729713	A549	lung:	n/a	n/a
34	TBP	chr11:107729251-107730072	GM12878	blood:	n/a	n/a
35	ZEB1	chr11:107728873-107729706	GM12878	blood:	n/a	n/a
36	TBP	chr11:107729144-107730127	K562	blood:	n/a	n/a
37	SIN3A	chr11:107728687-107730673	H1-hESC	embryonic stem cell:	n/a	chr11:107729330-107729341
38	POLR2A	chr11:107728707-107730103	K562	blood:	n/a	n/a
39	GABPA	chr11:107729212-107729786	K562	blood:	n/a	chr11:107729316-107729325
40	POLR2A	chr11:107728998-107730209	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr11:107728999-107730139	MCF-7	breast:	n/a	n/a
42	NR2F2	chr11:107728681-107730219	K562	blood:	n/a	n/a
43	TAF1	chr11:107729186-107729749	GM12891	blood:	n/a	n/a
44	REST	chr11:107729072-107729759	K562	blood:	n/a	chr11:107729325-107729338
45	POLR2A	chr11:107729176-107729748	U87	brain:	n/a	n/a
46	POLR2A	chr11:107729112-107730172	PANC-1	pancreas:	n/a	n/a
47	RFX5	chr11:107729264-107729985	GM12878	blood:	n/a	n/a
48	HEY1	chr11:107729052-107730021	K562	blood:	n/a	chr11:107729337-107729352 chr11:107729329-107729344
49	POLR2A	chr11:107729289-107730061	HCT-116	colon:	n/a	n/a
50	MAX	chr11:107728821-107729858	HepG2	liver:	n/a	chr11:107729315-107729322 chr11:107729341-107729350 chr11:107729314-107729323

No.	Distal block	Cell Line	Cell type
1	chr11:107728941..107731899-chr11:107878493..107880123,2	K562	blood:
2	chr11:107459711..107461881-chr11:107729122..107732071,2	K562	blood:
3	chr11:107728987..107729897-chr17:56736078..56736791,2	MCF-7	breast:

Variant related genes	Relation type
SLC35F2	TF binding region
ENSG00000202077	Chromatin interaction
ENSG00000166266	Chromatin interaction
ENSG00000110675	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2442684	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2456080	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3105399	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs480641	0.94[EUR][1000 genomes]
rs483463	0.82[CEU][hapmap]
rs488030	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs488081	0.82[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs488512	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs493037	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs502253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs502398	0.87[MEX][hapmap]
rs542931	0.80[ASW][hapmap];0.85[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs543568	0.84[CEU][hapmap];0.89[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs564569	0.82[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs565438	0.82[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs566238	0.82[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs575008	1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs578300	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs587130	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs651531	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs660042	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs668785	0.96[CEU][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs676108	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1039425	chr11:107468681-107895836	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv427899	chr11:107471544-107805894	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049524	chr11:107540937-107954011	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1038581	chr11:107564274-107838386	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv898378	chr11:107580985-107847983	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv521771	chr11:107590335-107904646	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1048938	chr11:107604473-107929950	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1045388	chr11:107686808-107733498	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv2750980	chr11:107720941-107970986	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv1043139	chr11:107725297-107869216	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv898381	chr11:107729106-107847983	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2442683	SLC35F2	cis	cerebellum	SCAN
rs2442683	FDX1	cis	parietal	SCAN
rs2442683	SLN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107727600-107730400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:107727600-107730400	Active TSS	NHEK	skin
3	chr11:107727600-107730800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:107727800-107730600	Active TSS	A549	lung
5	chr11:107727800-107730800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:107727800-107730800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:107727800-107731000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr11:107727800-107731200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:107728000-107729800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:107728000-107730400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr11:107728000-107730400	Active TSS	GM12878-XiMat	blood
12	chr11:107728000-107730800	Active TSS	Esophagus	oesophagus
13	chr11:107728200-107730400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:107728400-107730000	Active TSS	Fetal Lung	lung
15	chr11:107728400-107730600	Active TSS	Colon Smooth Muscle	Colon
16	chr11:107728400-107730600	Active TSS	Gastric	stomach
17	chr11:107728400-107730800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:107728400-107730800	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr11:107728400-107730800	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr11:107728400-107730800	Active TSS	Duodenum Mucosa	Duodenum
21	chr11:107728400-107730800	Active TSS	Ovary	ovary
22	chr11:107728400-107731000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:107728600-107729800	Active TSS	Pancreas	Pancrea
24	chr11:107728600-107730000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:107728600-107730000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
26	chr11:107728600-107730200	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr11:107728600-107730400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr11:107728600-107730400	Active TSS	HUVEC	blood vessel
29	chr11:107728600-107730400	Active TSS	K562	blood
30	chr11:107728600-107730600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:107728600-107730600	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr11:107728600-107730600	Active TSS	Brain Cingulate Gyrus	brain
33	chr11:107728600-107730600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr11:107728600-107730800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:107728600-107730800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr11:107728600-107730800	Active TSS	Fetal Kidney	kidney
37	chr11:107728600-107730800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr11:107728600-107730800	Active TSS	Right Ventricle	heart
39	chr11:107728600-107730800	Active TSS	Hela-S3	cervix
40	chr11:107728600-107730800	Active TSS	HMEC	breast
41	chr11:107728600-107730800	Active TSS	HSMM	muscle
42	chr11:107728600-107731000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:107728600-107731000	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr11:107728600-107731000	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr11:107728600-107731000	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr11:107728800-107729800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:107728800-107730000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr11:107728800-107730000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr11:107728800-107730000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr11:107728800-107730200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood

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