Variant report

Variant	rs10496046
Chromosome Location	chr2:55850905-55850906
allele	A/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	POLR2A	chr2:55850818-55851390	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55843280..55846696-chr2:55847912..55852861,6	MCF-7	breast:
2	chr2:55848892..55851384-chr2:55854717..55856988,2	MCF-7	breast:

Variant related genes	Relation type
SMEK2	TF binding region
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10469932	1.00[LWK][hapmap]
rs17278127	0.81[EUR][1000 genomes]
rs17736028	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17736159	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17736300	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17744287	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17744399	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17792467	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17792539	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17792972	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35232864	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3748950	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56043131	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56098806	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58321554	0.81[AFR][1000 genomes]
rs59722606	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60555175	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73940015	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73940017	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73940018	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73942925	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73942928	0.84[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	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55851600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:55846600-55852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
9	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:55846800-55851200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:55846800-55853000	Weak transcription	A549	lung
13	chr2:55846800-55858200	Weak transcription	HSMM	muscle
14	chr2:55846800-55862000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:55846800-55862000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:55846800-55862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:55846800-55862600	Weak transcription	NHDF-Ad	bronchial
18	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
19	chr2:55846800-55863400	Weak transcription	NHLF	lung
20	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:55847000-55852600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr2:55847400-55852400	Weak transcription	HMEC	breast
24	chr2:55847400-55852800	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr2:55847400-55859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:55847400-55862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:55847600-55852400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:55847600-55852600	Weak transcription	Brain Anterior Caudate	brain
30	chr2:55847600-55852600	Weak transcription	Right Atrium	heart
31	chr2:55847600-55857400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:55847600-55860800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:55847600-55862000	Weak transcription	Osteobl	bone
34	chr2:55847600-55864200	Weak transcription	Brain Germinal Matrix	brain
35	chr2:55847600-55870000	Weak transcription	Colonic Mucosa	Colon
36	chr2:55847600-55870000	Weak transcription	Psoas Muscle	Psoas
37	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
38	chr2:55847800-55852400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:55847800-55852400	Weak transcription	NHEK	skin
40	chr2:55847800-55852600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:55847800-55859000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:55847800-55862000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:55847800-55862000	Weak transcription	NH-A	brain
44	chr2:55847800-55862200	Weak transcription	HUVEC	blood vessel
45	chr2:55847800-55863400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:55848000-55853200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr2:55848000-55856800	Weak transcription	Brain Angular Gyrus	brain
48	chr2:55848000-55862600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:55848000-55862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:55848000-55872600	Weak transcription	Small Intestine	intestine

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