Variant report

Variant	rs7425883
Chromosome Location	chr2:98331521-98331522
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98269672..98271940-chr2:98331175..98333496,2	K562	blood:
2	chr2:98330772..98333242-chr2:98334688..98336662,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12999616	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17028771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17031009	0.90[YRI][hapmap]
rs17695937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071038	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290123	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290126	0.94[ASN][1000 genomes]
rs2290127	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34459720	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35321033	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35530168	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35958372	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55757705	1.00[ASN][1000 genomes]
rs55766309	1.00[ASN][1000 genomes]
rs55933640	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56035334	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56233535	1.00[ASN][1000 genomes]
rs56717024	1.00[ASN][1000 genomes]
rs58321192	0.94[ASN][1000 genomes]
rs58383658	0.86[ASN][1000 genomes]
rs59021370	0.94[ASN][1000 genomes]
rs59060391	0.94[ASN][1000 genomes]
rs59168350	1.00[ASN][1000 genomes]
rs62157581	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542982	1.00[ASN][1000 genomes]
rs6753752	1.00[ASN][1000 genomes]
rs72951131	0.94[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	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874696	chr2:98309882-98362907	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv33510	chr2:98317103-98341302	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7425883	LOC375249	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98326200-98333000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:98329000-98331600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:98329000-98331600	Enhancers	Fetal Muscle Trunk	muscle
4	chr2:98329000-98331800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr2:98329000-98336000	Enhancers	Fetal Muscle Leg	muscle
6	chr2:98329400-98332000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr2:98329600-98331800	Active TSS	Colonic Mucosa	Colon
8	chr2:98329800-98332400	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr2:98330000-98331600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:98330000-98332400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:98330000-98337200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:98330200-98332000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:98330200-98332000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:98330200-98332200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
15	chr2:98330200-98334800	Weak transcription	GM12878-XiMat	blood
16	chr2:98330200-98335800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:98330400-98333600	Transcr. at gene 5' and 3'	Dnd41	blood
18	chr2:98330600-98331800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:98330800-98331800	Enhancers	HMEC	breast
20	chr2:98330800-98331800	Enhancers	NHEK	skin
21	chr2:98330800-98332000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:98330800-98332800	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr2:98330800-98333000	Weak transcription	Spleen	Spleen
24	chr2:98330800-98334400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:98330800-98336000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
26	chr2:98331000-98331600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr2:98331000-98331800	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
28	chr2:98331000-98333000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr2:98331000-98334200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:98331200-98331600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:98331200-98332400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:98331200-98333800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:98331200-98334800	Weak transcription	Primary B cells from cord blood	blood
34	chr2:98331200-98335000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
35	chr2:98331200-98335800	Transcr. at gene 5' and 3'	Thymus	Thymus
36	chr2:98331200-98337200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:98331400-98331800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr2:98331400-98331800	Weak transcription	Esophagus	oesophagus
39	chr2:98331400-98332400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:98331400-98332600	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:98331400-98333600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr2:98331400-98333600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr2:98331400-98334600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:98331400-98336000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:98331400-98336200	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood

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