Variant report

Variant	rs12987410
Chromosome Location	chr2:113938089-113938090
allele	C/G
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	MAZ	chr2:113937944-113938250	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:113937624-113938359	GM12878	blood:	n/a	n/a
3	HNF4A	chr2:113937923-113938380	HepG2	liver:	n/a	n/a
4	ZBTB7A	chr2:113937962-113938358	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:113937896-113938363	HepG2	liver:	n/a	n/a
6	ELF1	chr2:113937854-113938386	HepG2	liver:	n/a	n/a
7	MAFK	chr2:113937854-113938304	HepG2	liver:	n/a	n/a
8	JUND	chr2:113938004-113938403	HepG2	liver:	n/a	chr2:113938194-113938205
9	CTCF	chr2:113938050-113938436	K562	blood:	n/a	n/a
10	FOSL2	chr2:113937882-113938433	HepG2	liver:	n/a	chr2:113938195-113938206
11	HNF4A	chr2:113937735-113938371	HepG2	liver:	n/a	n/a
12	RAD21	chr2:113938018-113938407	HepG2	liver:	n/a	n/a
13	RAD21	chr2:113937891-113938487	HepG2	liver:	n/a	n/a
14	MAX	chr2:113937983-113938494	K562	blood:	n/a	chr2:113938358-113938369 chr2:113938360-113938369
15	MYBL2	chr2:113937498-113938579	HepG2	liver:	n/a	n/a
16	BHLHE40	chr2:113937914-113938336	HepG2	liver:	n/a	n/a
17	RFX5	chr2:113938026-113938315	HepG2	liver:	n/a	n/a
18	CTCF	chr2:113938063-113938387	HepG2	liver:	n/a	n/a
19	NR2F2	chr2:113937979-113938498	K562	blood:	n/a	n/a
20	NFIC	chr2:113937823-113938375	HepG2	liver:	n/a	n/a
21	MYBL2	chr2:113937603-113938438	HepG2	liver:	n/a	n/a
22	NFIC	chr2:113937663-113938553	HepG2	liver:	n/a	n/a
23	JUND	chr2:113937975-113938355	HepG2	liver:	n/a	chr2:113938194-113938205
24	POLR2A	chr2:113937893-113938286	HepG2	liver:	n/a	n/a
25	HEY1	chr2:113937806-113938485	HepG2	liver:	n/a	n/a
26	FOSL2	chr2:113937699-113938456	HepG2	liver:	n/a	chr2:113938195-113938206
27	MAX	chr2:113937616-113938608	HepG2	liver:	n/a	chr2:113937676-113937685 chr2:113938358-113938369 chr2:113938360-113938369
28	MAX	chr2:113937931-113938475	HepG2	liver:	n/a	chr2:113938358-113938369 chr2:113938360-113938369
29	ZBTB7A	chr2:113938051-113938344	K562	blood:	n/a	n/a
30	HNF4A	chr2:113937959-113938345	HepG2	liver:	n/a	n/a
31	CTCF	chr2:113938089-113938432	HepG2	liver:	n/a	n/a
32	EP300	chr2:113937996-113938246	HepG2	liver:	n/a	n/a
33	REST	chr2:113937867-113938334	HepG2	liver:	n/a	n/a
34	ELF1	chr2:113937975-113938380	K562	blood:	n/a	n/a
35	ZBTB7A	chr2:113938058-113938348	HepG2	liver:	n/a	n/a
36	POLR2A	chr2:113937862-113938295	HepG2	liver:	n/a	n/a
37	TBP	chr2:113937983-113938239	HepG2	liver:	n/a	n/a
38	YY1	chr2:113937664-113938323	HepG2	liver:	n/a	n/a
39	RAD21	chr2:113937987-113938401	HepG2	liver:	n/a	n/a
40	POLR2A	chr2:113937702-113938372	GM12891	blood:	n/a	n/a
41	POLR2A	chr2:113937956-113938370	K562	blood:	n/a	n/a
42	JUN	chr2:113938035-113938281	HepG2	liver:	n/a	n/a
43	ELF1	chr2:113937911-113938301	GM12878	blood:	n/a	n/a
44	CHD2	chr2:113937938-113938186	HepG2	liver:	n/a	n/a
45	FOXA1	chr2:113937752-113938438	HepG2	liver:	n/a	n/a
46	HNF4G	chr2:113937829-113938505	HepG2	liver:	n/a	n/a
47	ELF1	chr2:113937990-113938359	HepG2	liver:	n/a	n/a
48	MAX	chr2:113937599-113938515	HepG2	liver:	n/a	chr2:113937676-113937685 chr2:113938358-113938369 chr2:113938360-113938369
49	SP1	chr2:113937812-113938440	HepG2	liver:	n/a	chr2:113938285-113938295 chr2:113938285-113938295
50	POLR2A	chr2:113935771-113938534	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113933965..113936589-chr2:113937925..113940404,2	MCF-7	breast:
2	chr2:113914767..113917449-chr2:113937885..113940587,3	MCF-7	breast:

Variant related genes	Relation type
PSD4	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13023682	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17624171	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17624793	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34949856	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34973738	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874897	chr2:113935407-113944762	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv874898	chr2:113935407-113954247	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113916000-113939000	Weak transcription	Right Atrium	heart
2	chr2:113923000-113951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:113923000-113956000	Weak transcription	HMEC	breast
4	chr2:113932400-113939400	Weak transcription	Fetal Stomach	stomach
5	chr2:113932400-113939600	Enhancers	Placenta	Placenta
6	chr2:113933000-113938800	Weak transcription	Adipose Nuclei	Adipose
7	chr2:113934200-113939000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:113934200-113949000	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr2:113934200-113956200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:113934400-113939600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr2:113934400-113940000	Genic enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:113934400-113948600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:113934600-113939000	Weak transcription	Colonic Mucosa	Colon
14	chr2:113934600-113939000	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:113934600-113940800	Genic enhancers	Fetal Thymus	thymus
16	chr2:113934600-113941000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:113934600-113946400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:113934800-113938600	Weak transcription	Fetal Lung	lung
19	chr2:113934800-113938800	Weak transcription	Lung	lung
20	chr2:113934800-113939000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:113934800-113939000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:113934800-113939400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:113934800-113939800	Genic enhancers	Thymus	Thymus
24	chr2:113935000-113939000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:113935200-113942800	Genic enhancers	Dnd41	blood
26	chr2:113935400-113938800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr2:113935800-113939800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:113936000-113938800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:113936200-113938200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
30	chr2:113936200-113939800	Enhancers	Primary hematopoietic stem cells	blood
31	chr2:113936400-113938800	Enhancers	K562	blood
32	chr2:113936600-113939000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:113936600-113939000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:113936600-113939000	Weak transcription	NHEK	skin
35	chr2:113936800-113939000	Enhancers	Spleen	Spleen
36	chr2:113936800-113940000	Enhancers	Liver	Liver
37	chr2:113936800-113940400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:113937000-113938800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr2:113937000-113938800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:113937200-113939000	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr2:113937400-113938200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:113937400-113938400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:113937400-113939000	Enhancers	Fetal Intestine Small	intestine
44	chr2:113937600-113938200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
45	chr2:113937600-113938400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:113937600-113939200	Enhancers	Esophagus	oesophagus
47	chr2:113937600-113939600	Enhancers	Fetal Muscle Leg	muscle
48	chr2:113937600-113939600	Flanking Active TSS	HepG2	liver
49	chr2:113937600-113940000	Enhancers	Gastric	stomach
50	chr2:113937800-113938200	Enhancers	HUES6 Cell Line	embryonic stem cell

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