Variant report

Variant	rs250227
Chromosome Location	chr5:50260568-50260569
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	REST	chr5:50258594-50260715	H1-neurons	neurons:	n/a	n/a
2	MXI1	chr5:50258469-50261560	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:50259720-50261031	H1-neurons	neurons:	n/a	n/a
4	RAD21	chr5:50258099-50260834	SK-N-SH	brain:	n/a	chr5:50258941-50258955 chr5:50258940-50258959
5	POLR2A	chr5:50259759-50261040	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:38003355..38005334-chr5:50260049..50263278,3	MCF-7	breast:
2	chr5:50260308..50260944-chr5:50571869..50572389,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PARP8-2	chr5:50260253-50261737	NONHSAT101376

Variant related genes	Relation type
ENSG00000248918	TF binding region
ENSG00000100083	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1354171	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1374037	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs173648	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs185136	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs192223	0.96[AFR][1000 genomes]
rs1993954	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250225	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250226	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250228	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250232	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250235	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250239	0.91[AFR][1000 genomes]
rs250240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250242	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250243	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs27276	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs31714	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs583124	0.87[AFR][1000 genomes]
rs583125	0.95[AFR][1000 genomes]
rs589372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs602484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs614328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs630982	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs679678	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830286	chr5:50165805-50374600	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50258600-50261600	Active TSS	Stomach Smooth Muscle	stomach
2	chr5:50258600-50266600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr5:50259000-50260600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr5:50259600-50260600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:50259600-50260600	Bivalent Enhancer	Fetal Brain Male	brain
6	chr5:50259600-50260600	Bivalent Enhancer	Fetal Intestine Small	intestine
7	chr5:50259600-50260800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:50259600-50260800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
9	chr5:50259800-50260600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
10	chr5:50260000-50260600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
11	chr5:50260000-50261000	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
12	chr5:50260200-50260600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:50260200-50260800	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:50260200-50260800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
15	chr5:50260200-50260800	Bivalent Enhancer	Brain Angular Gyrus	brain
16	chr5:50260200-50261400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr5:50260200-50265000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:50260400-50260600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
19	chr5:50260400-50260600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:50260400-50260600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
21	chr5:50260400-50260600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
22	chr5:50260400-50260800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
23	chr5:50260400-50260800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
24	chr5:50260400-50261800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:50260400-50261800	Weak transcription	Pancreas	Pancrea
26	chr5:50260400-50262000	Weak transcription	Right Atrium	heart

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