Variant report

Variant	rs9838458
Chromosome Location	chr3:120470070-120470071
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	chr3:120459863..120463133-chr3:120465920..120470912,5	K562	blood:
2	chr3:120469262..120472636-chr3:120473122..120476515,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153767	Chromatin interaction
ENSG00000144840	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10511404	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11714961	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489104	0.84[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs13316584	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1566988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs167722	0.86[ASN][1000 genomes]
rs172819	0.83[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs178725	0.87[ASN][1000 genomes]
rs2288096	0.84[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs2292719	0.82[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];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373188	0.87[ASN][1000 genomes]
rs417061	0.83[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4501055	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs519336	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs55831173	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56406902	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607953	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs618642	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs6778859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6796222	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73183726	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7430785	1.00[YRI][hapmap]
rs7620570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633399	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872831	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9985346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][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	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1005396	chr3:120460741-120580319	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	esv1797756	chr3:120464660-120473719	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv829700	chr3:120469191-120675763	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9838458	ALDH1L1	cis	parietal	SCAN
rs9838458	FSTL1	cis	parietal	SCAN
rs9838458	STXBP5L	cis	cerebellum	SCAN
rs9838458	SLC41A3	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120462400-120471400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:120462600-120495200	Weak transcription	Aorta	Aorta
3	chr3:120462800-120472200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:120462800-120473000	Weak transcription	Brain Anterior Caudate	brain
5	chr3:120462800-120483000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:120462800-120485600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:120462800-120499800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:120462800-120500000	Weak transcription	Gastric	stomach
9	chr3:120462800-120503000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:120463000-120472000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:120463000-120472000	Weak transcription	Stomach Mucosa	stomach
12	chr3:120463000-120472600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:120463000-120473200	Weak transcription	NHLF	lung
14	chr3:120463000-120477800	Weak transcription	Spleen	Spleen
15	chr3:120463000-120482400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:120463000-120484800	Weak transcription	K562	blood
17	chr3:120463000-120485600	Weak transcription	Pancreas	Pancrea
18	chr3:120463000-120485600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:120463000-120485600	Weak transcription	HMEC	breast
20	chr3:120463000-120493600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:120463000-120496000	Weak transcription	Fetal Lung	lung
22	chr3:120463000-120499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:120463000-120502000	Weak transcription	Colonic Mucosa	Colon
24	chr3:120463000-120504200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:120463000-120504800	Weak transcription	Fetal Brain Male	brain
26	chr3:120463200-120472600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:120463200-120473200	Weak transcription	Fetal Heart	heart
28	chr3:120463200-120474600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:120463200-120484600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:120463200-120485400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:120463200-120492000	Weak transcription	Thymus	Thymus
32	chr3:120463200-120494000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:120463200-120495200	Weak transcription	Fetal Intestine Small	intestine
34	chr3:120463400-120470800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:120463400-120472800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:120463400-120474000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:120463400-120476800	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:120463400-120478800	Weak transcription	NH-A	brain
39	chr3:120463400-120482800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:120463400-120485000	Weak transcription	Brain Angular Gyrus	brain
41	chr3:120463400-120497000	Weak transcription	Fetal Kidney	kidney
42	chr3:120463400-120503000	Weak transcription	Small Intestine	intestine
43	chr3:120464000-120489600	Weak transcription	NHDF-Ad	bronchial
44	chr3:120466800-120473400	Weak transcription	Brain Germinal Matrix	brain
45	chr3:120466800-120481400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:120469200-120471000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:120469200-120471200	Strong transcription	Hela-S3	cervix
48	chr3:120469200-120471400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:120469200-120471600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:120469200-120472000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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