Variant report

Variant	rs287998
Chromosome Location	chr2:9999357-9999358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9998951..10002635-chr2:10014006..10016302,3	K562	blood:
2	chr2:9999348..10001334-chr2:10185106..10187713,2	K562	blood:
3	chr2:9982413..9984007-chr2:9997809..10000027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12612554	0.91[ASW][hapmap];0.85[AFR][1000 genomes]
rs1652684	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs287984	0.89[MKK][hapmap]
rs287985	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs288000	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs288001	0.83[AFR][1000 genomes]
rs366852	0.82[AFR][1000 genomes]
rs379396	0.85[AFR][1000 genomes]
rs385513	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs386006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs393281	0.92[ASW][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs394952	0.88[AFR][1000 genomes]
rs396190	0.85[AFR][1000 genomes]
rs396416	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs400098	0.92[ASW][hapmap];0.82[AFR][1000 genomes]
rs403303	1.00[ASW][hapmap];0.87[AFR][1000 genomes]
rs406546	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs417748	0.85[AFR][1000 genomes]
rs419453	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs446907	0.87[AFR][1000 genomes]
rs448327	1.00[ASW][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs6744203	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv873629	chr2:9949464-10016627	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
5	nsv873630	chr2:9953949-10030024	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	nsv873631	chr2:9975557-10059770	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
7	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv580960	chr2:9993451-10066694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9985000-10000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:9987200-10038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:9987400-10003200	Weak transcription	Stomach Mucosa	stomach
4	chr2:9989400-10000600	Strong transcription	Muscle Satellite Cultured Cells	--
5	chr2:9989400-10001000	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:9989600-9999400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:9989600-10001200	Strong transcription	Osteobl	bone
8	chr2:9990400-10000600	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr2:9990400-10000800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:9990600-10000800	Strong transcription	Stomach Smooth Muscle	stomach
11	chr2:9990600-10001600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:9993000-10003600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:9993200-10001200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:9993600-10007400	Weak transcription	Psoas Muscle	Psoas
15	chr2:9993800-10002600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr2:9993800-10002800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:9993800-10079600	Weak transcription	Gastric	stomach
18	chr2:9994600-10000600	Weak transcription	Right Ventricle	heart
19	chr2:9995400-10001200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr2:9995400-10002600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:9995400-10002800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:9995600-10002600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr2:9995800-10001200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
24	chr2:9995800-10001400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr2:9995800-10038000	Weak transcription	Small Intestine	intestine
26	chr2:9996000-10001200	ZNF genes & repeats	Fetal Brain Female	brain
27	chr2:9996000-10001200	ZNF genes & repeats	Dnd41	blood
28	chr2:9996000-10001600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:9996200-10001000	ZNF genes & repeats	A549	lung
30	chr2:9996400-10001600	ZNF genes & repeats	Brain Germinal Matrix	brain
31	chr2:9996400-10016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:9996600-10001400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:9996800-10001400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:9996800-10001400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:9997000-10001000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr2:9997000-10001600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
37	chr2:9997000-10002600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:9997200-9999400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:9997200-10001000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:9997200-10001400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
41	chr2:9997200-10001400	ZNF genes & repeats	Primary B cells from cord blood	blood
42	chr2:9997200-10001400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr2:9997400-9999400	ZNF genes & repeats	NHEK	skin
44	chr2:9997400-10001200	ZNF genes & repeats	Fetal Lung	lung
45	chr2:9997400-10001400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
46	chr2:9997400-10001400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr2:9997400-10001400	ZNF genes & repeats	Thymus	Thymus
48	chr2:9997400-10002000	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr2:9997600-10001400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
50	chr2:9997600-10001600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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