Variant report

Variant	rs965892
Chromosome Location	chr9:93629789-93629790
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	chr9:93628438..93632863-chr9:93633146..93636625,4	K562	blood:
2	chr9:93619506..93622175-chr9:93629106..93631175,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs158508	1.00[CHB][hapmap]
rs1755958	1.00[CHB][hapmap]
rs1760124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1760125	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2035072	1.00[CHB][hapmap]
rs2613310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613320	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs2774257	0.81[EUR][1000 genomes]
rs2780710	0.82[EUR][1000 genomes]
rs290203	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs290204	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs290213	1.00[CHB][hapmap]
rs290224	1.00[ASN][1000 genomes]
rs290225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290232	1.00[CHB][hapmap]
rs290234	1.00[CHB][hapmap]
rs290235	1.00[CHB][hapmap]
rs290236	1.00[CHB][hapmap]
rs290237	1.00[CHB][hapmap]
rs290238	1.00[CHB][hapmap]
rs290256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290257	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991216	0.81[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs914928	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs914929	1.00[JPT][hapmap]

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	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1039761	chr9:93598856-93677831	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv430078	chr9:93609668-93642766	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1053252	chr9:93610132-93699103	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv430079	chr9:93620963-93642766	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs965892	GADD45G	cis	cerebellum	SCAN
rs965892	JAGN1	trans	parietal	SCAN
rs965892	SPTLC1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93601800-93642200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:93605000-93633000	Weak transcription	Fetal Kidney	kidney
3	chr9:93605800-93631000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr9:93611200-93642200	Weak transcription	Stomach Mucosa	stomach
5	chr9:93617200-93640600	Weak transcription	K562	blood
6	chr9:93617400-93640600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:93617800-93640600	Weak transcription	NHEK	skin
8	chr9:93619400-93630000	Strong transcription	Thymus	Thymus
9	chr9:93621200-93631400	Strong transcription	Primary B cells from cord blood	blood
10	chr9:93622600-93631200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr9:93622800-93630000	Strong transcription	Fetal Stomach	stomach
12	chr9:93623200-93630000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr9:93623200-93630800	Strong transcription	GM12878-XiMat	blood
14	chr9:93623600-93631200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr9:93623600-93642400	Weak transcription	Adipose Nuclei	Adipose
16	chr9:93623800-93630400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr9:93623800-93631000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:93623800-93631400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr9:93624000-93630000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:93624000-93631200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr9:93624200-93630000	Strong transcription	Fetal Intestine Large	intestine
22	chr9:93625000-93636600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:93625000-93642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:93625200-93642400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:93625600-93636400	Weak transcription	Lung	lung
26	chr9:93625800-93635800	Weak transcription	Esophagus	oesophagus
27	chr9:93626000-93647800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr9:93626800-93631200	Strong transcription	Primary hematopoietic stem cells	blood
29	chr9:93627400-93630600	Strong transcription	Fetal Thymus	thymus
30	chr9:93627400-93631400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:93627600-93630000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:93627600-93631200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:93627600-93636400	Weak transcription	Small Intestine	intestine
34	chr9:93628400-93630000	Strong transcription	Fetal Intestine Small	intestine
35	chr9:93628400-93630000	Strong transcription	Spleen	Spleen
36	chr9:93628600-93629800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr9:93629200-93629800	Strong transcription	Colonic Mucosa	Colon
38	chr9:93629200-93630000	Strong transcription	Pancreas	Pancrea
39	chr9:93629200-93640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:93629400-93630000	Strong transcription	Gastric	stomach
41	chr9:93629600-93629800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:93629600-93639400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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