Variant report

Variant	rs4296785
Chromosome Location	chr5:75710783-75710784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75706305..75708595-chr5:75709828..75711425,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10065322	0.90[ASN][1000 genomes]
rs10068651	0.80[YRI][hapmap]
rs10213849	0.80[YRI][hapmap]
rs10462539	0.85[ASN][1000 genomes]
rs10462540	0.86[ASN][1000 genomes]
rs11738470	0.82[ASN][1000 genomes]
rs11740038	0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs11743541	0.80[YRI][hapmap]
rs11744637	0.90[ASN][1000 genomes]
rs11747990	0.90[ASN][1000 genomes]
rs13357820	0.84[ASN][1000 genomes]
rs28386181	0.88[ASN][1000 genomes]
rs3886042	0.86[ASN][1000 genomes]
rs3886043	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4254886	0.90[ASN][1000 genomes]
rs4501323	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704310	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995866	0.85[ASN][1000 genomes]
rs6453217	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6895725	0.84[ASN][1000 genomes]
rs7706926	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs7707426	0.90[ASN][1000 genomes]
rs7718641	0.90[ASN][1000 genomes]
rs7731240	0.90[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	nsv870415	chr5:75526088-75738412	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv882206	chr5:75676658-75746813	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4296785	RGNEF	cis	parietal	SCAN
rs4296785	TNPO1	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75701000-75721600	Weak transcription	Fetal Stomach	stomach
2	chr5:75701600-75713000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:75703000-75731800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:75703200-75717800	Weak transcription	Small Intestine	intestine
5	chr5:75703400-75715600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:75703400-75718000	Weak transcription	Primary T cells from cord blood	blood
7	chr5:75703600-75747000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:75704600-75716800	Weak transcription	Fetal Intestine Small	intestine
9	chr5:75706000-75712200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:75706800-75718000	Weak transcription	Fetal Lung	lung
11	chr5:75707000-75727600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:75707800-75711600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:75707800-75717600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:75707800-75718000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:75708400-75711000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr5:75708600-75710800	Enhancers	Gastric	stomach
17	chr5:75708600-75710800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr5:75709200-75710800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr5:75709600-75712200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:75709800-75711400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:75709800-75712000	Enhancers	Liver	Liver
22	chr5:75709800-75712200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:75709800-75718000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:75709800-75727200	Weak transcription	Primary B cells from cord blood	blood
25	chr5:75710200-75711600	Enhancers	HepG2	liver
26	chr5:75710200-75712000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr5:75710200-75715400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr5:75710200-75715800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr5:75710200-75717000	Weak transcription	Pancreas	Pancrea
30	chr5:75710200-75719000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:75710200-75720600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:75710200-75720800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr5:75710600-75711000	Enhancers	Stomach Mucosa	stomach
34	chr5:75710600-75711400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:75710600-75712600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr5:75710600-75716600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr5:75710600-75718000	Weak transcription	Primary hematopoietic stem cells	blood

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