Variant report

Variant	rs3112988
Chromosome Location	chr2:95744882-95744883
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:95742738..95745180-chr2:95770286..95773157,2	MCF-7	breast:
2	chr2:95744437..95746495-chr2:95786116..95787927,2	MCF-7	breast:
3	chr2:95722359..95726880-chr2:95740082..95744931,5	MCF-7	breast:
4	chr2:95687762..95688372-chr2:95744421..95745392,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144029	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2291991	0.81[ASN][1000 genomes]
rs2320619	0.81[ASN][1000 genomes]
rs2320620	0.82[ASN][1000 genomes]
rs3105100	0.93[ASN][1000 genomes]
rs3105101	0.95[ASN][1000 genomes]
rs3112225	0.81[ASN][1000 genomes]
rs3112228	0.81[ASN][1000 genomes]
rs3112231	0.80[ASN][1000 genomes]
rs3112982	0.81[ASN][1000 genomes]
rs3112984	0.88[ASN][1000 genomes]
rs3112985	0.87[ASN][1000 genomes]
rs3112986	0.87[ASN][1000 genomes]
rs3112987	0.81[ASN][1000 genomes]
rs3112990	0.92[ASN][1000 genomes]
rs4854243	0.81[ASN][1000 genomes]
rs4854244	0.86[ASN][1000 genomes]
rs7585473	0.91[ASN][1000 genomes]
rs872580	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv963662	chr2:95739492-95770323	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95742800-95745800	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr2:95742800-95746000	Enhancers	Primary T cells from cord blood	blood
3	chr2:95743000-95745400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:95743000-95745600	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr2:95743000-95745800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr2:95743000-95750800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:95743000-95751000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:95743000-95751000	Weak transcription	Primary B cells from cord blood	blood
9	chr2:95743000-95751200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:95743000-95753000	Weak transcription	Spleen	Spleen
11	chr2:95743000-95759400	Weak transcription	Right Atrium	heart
12	chr2:95743000-95770200	Weak transcription	Psoas Muscle	Psoas
13	chr2:95743200-95745000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:95743200-95745800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:95743200-95745800	Enhancers	Fetal Thymus	thymus
16	chr2:95743200-95746000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr2:95743200-95746000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:95743200-95750000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:95743200-95750200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:95743200-95750600	Weak transcription	HMEC	breast
21	chr2:95743200-95750800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:95743200-95750800	Weak transcription	Right Ventricle	heart
23	chr2:95743200-95751000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:95743200-95751000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:95743200-95753000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:95743200-95753000	Weak transcription	Colonic Mucosa	Colon
27	chr2:95743400-95745200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr2:95743400-95745200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:95743400-95745400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr2:95743400-95745800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr2:95743400-95750800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:95743400-95751000	Weak transcription	Liver	Liver
33	chr2:95743400-95751000	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:95743400-95751000	Weak transcription	Lung	lung
35	chr2:95743400-95751200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:95743400-95751200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:95743400-95751200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:95743400-95751400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:95743400-95752000	Weak transcription	GM12878-XiMat	blood
40	chr2:95743400-95752600	Weak transcription	K562	blood
41	chr2:95743400-95753000	Weak transcription	Pancreas	Pancrea
42	chr2:95743600-95745800	Enhancers	Thymus	Thymus
43	chr2:95743600-95750800	Weak transcription	Brain Angular Gyrus	brain
44	chr2:95743600-95751200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:95743600-95751200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:95743800-95745000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:95744000-95745000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:95744000-95745000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr2:95744000-95745000	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr2:95744000-95745000	Weak transcription	Brain Inferior Temporal Lobe	brain

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