Variant report

Variant	rs12999225
Chromosome Location	chr2:99388885-99388886
allele	G/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	TBP	chr2:99388107-99388906	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:99387967-99388920	GM12892	blood:	n/a	n/a
3	MAX	chr2:99388124-99388905	NB4	blood:	n/a	n/a
4	POLR2A	chr2:99387992-99388888	GM12892	blood:	n/a	n/a
5	RUNX3	chr2:99388054-99388992	GM12878	blood:	n/a	chr2:99388648-99388665
6	POLR2A	chr2:99384652-99389971	K562	blood:	n/a	n/a
7	MTA3	chr2:99387967-99389029	GM12878	blood:	n/a	n/a
8	MTA3	chr2:99388015-99389083	GM12878	blood:	n/a	n/a
9	RUNX3	chr2:99388108-99389140	GM12878	blood:	n/a	chr2:99388648-99388665
10	EBF1	chr2:99388607-99389079	GM12878	blood:	n/a	chr2:99388971-99388982
11	WRNIP1	chr2:99388298-99388960	GM12878	blood:	n/a	n/a
12	BHLHE40	chr2:99388541-99388889	GM12878	blood:	n/a	n/a
13	NFIC	chr2:99388206-99389065	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:99388483-99389023	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99344922..99348721-chr2:99382903..99389092,6	MCF-7	breast:
2	chr2:99345368..99349321-chr2:99385005..99390572,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226791	TF binding region
ENSG00000071073	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10166044	0.83[ASN][1000 genomes]
rs10189330	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615689	0.89[EUR][1000 genomes]
rs13389386	0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1356424	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2276604	0.87[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2280256	0.81[JPT][hapmap]
rs6712597	0.84[ASN][1000 genomes]
rs6716514	0.84[ASN][1000 genomes]
rs6733011	0.80[EUR][1000 genomes]
rs6757099	0.82[ASN][1000 genomes]
rs7557295	0.86[ASN][1000 genomes]
rs7570815	0.86[ASN][1000 genomes]
rs7578035	0.89[EUR][1000 genomes]
rs7581128	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7581349	0.90[EUR][1000 genomes]
rs7582382	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9308815	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99378400-99389400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:99384400-99389800	Flanking Active TSS	Dnd41	blood
3	chr2:99385000-99389400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr2:99385800-99394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:99385800-99410400	Weak transcription	Right Atrium	heart
6	chr2:99386200-99389000	Flanking Active TSS	Fetal Thymus	thymus
7	chr2:99386200-99389200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr2:99386200-99391600	Weak transcription	Fetal Brain Female	brain
9	chr2:99386400-99389000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr2:99386600-99391000	Weak transcription	Fetal Brain Male	brain
11	chr2:99386800-99391400	Weak transcription	Esophagus	oesophagus
12	chr2:99387400-99389000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr2:99387400-99389000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr2:99387400-99389000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:99387400-99389200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:99387400-99389200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:99387400-99389400	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr2:99387400-99389600	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:99387600-99389000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:99387600-99389000	Flanking Active TSS	GM12878-XiMat	blood
21	chr2:99387600-99389400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr2:99387600-99392000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:99387800-99389200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr2:99387800-99389800	Enhancers	Fetal Muscle Leg	muscle
25	chr2:99387800-99390200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:99388000-99389000	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr2:99388000-99389600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr2:99388000-99389800	Enhancers	Spleen	Spleen
29	chr2:99388000-99391400	Weak transcription	Pancreas	Pancrea
30	chr2:99388200-99389000	Active TSS	Stomach Smooth Muscle	stomach
31	chr2:99388200-99389000	Enhancers	HepG2	liver
32	chr2:99388200-99389400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:99388200-99389400	Enhancers	HMEC	breast
34	chr2:99388200-99389400	Bivalent Enhancer	Osteobl	bone
35	chr2:99388400-99389000	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr2:99388400-99389200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:99388400-99389400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:99388400-99389400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:99388400-99389400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:99388400-99389600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:99388600-99389000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:99388600-99389200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:99388600-99389200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr2:99388600-99389400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr2:99388600-99389400	Enhancers	Brain Anterior Caudate	brain
46	chr2:99388600-99389600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:99388600-99389600	Enhancers	Brain Substantia Nigra	brain
48	chr2:99388600-99389600	Enhancers	Placenta	Placenta
49	chr2:99388600-99392200	Weak transcription	Lung	lung
50	chr2:99388800-99389000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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