Variant report

Variant	rs9812438
Chromosome Location	chr3:98535614-98535615
allele	C/T
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	POLR2A	chr3:98532422-98540691	U87	brain:	n/a	n/a
2	POLR2A	chr3:98531678-98540691	U87	brain:	n/a	n/a
3	POLR2A	chr3:98530977-98539024	U87	brain:	n/a	n/a
4	POLR2A	chr3:98530971-98537862	U87	brain:	n/a	n/a

Variant related genes	Relation type
DCBLD2	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10084679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330381	0.85[AMR][1000 genomes]
rs13317610	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13318960	0.85[AMR][1000 genomes]
rs13320266	0.88[ASN][1000 genomes]
rs13320890	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs13322253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28417568	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429424	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28489284	0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528154	0.85[AMR][1000 genomes]
rs28650813	0.85[AMR][1000 genomes]
rs3796133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56172805	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56857413	0.82[ASN][1000 genomes]
rs57962467	0.82[ASN][1000 genomes]
rs59906228	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72932691	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72932700	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72934623	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72938577	0.82[ASN][1000 genomes]
rs9289699	0.85[AMR][1000 genomes]
rs9289700	0.85[AMR][1000 genomes]
rs9810407	0.88[ASN][1000 genomes]
rs9818215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9833945	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9836437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9836915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9838166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9838238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9838706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839559	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9848335	0.85[AMR][1000 genomes]
rs9848583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9862660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870500	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9870940	0.85[AMR][1000 genomes]
rs9879302	0.85[AMR][1000 genomes]
rs9883751	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
4	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
5	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:98524200-98544200	Strong transcription	HSMM	muscle
8	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
9	chr3:98526200-98543200	Weak transcription	Lung	lung
10	chr3:98526400-98536000	Weak transcription	Aorta	Aorta
11	chr3:98526400-98538200	Weak transcription	GM12878-XiMat	blood
12	chr3:98526400-98539200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:98526400-98539400	Weak transcription	Fetal Brain Male	brain
14	chr3:98526400-98542800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:98526400-98544200	Weak transcription	Brain Angular Gyrus	brain
16	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
17	chr3:98526600-98537400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:98526600-98539000	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:98526600-98540000	Weak transcription	Fetal Thymus	thymus
20	chr3:98527000-98536600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:98527000-98536600	Weak transcription	K562	blood
22	chr3:98527000-98538600	Weak transcription	Primary T cells from cord blood	blood
23	chr3:98527200-98536600	Weak transcription	Brain Anterior Caudate	brain
24	chr3:98527200-98536600	Weak transcription	Brain Germinal Matrix	brain
25	chr3:98527200-98542200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:98527200-98545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:98527200-98545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:98528400-98542200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:98528600-98543600	Strong transcription	NHEK	skin
31	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:98529000-98540000	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:98529200-98536600	Weak transcription	Fetal Heart	heart
34	chr3:98529200-98538200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:98529400-98539000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:98529400-98546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:98530400-98535800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:98530400-98537400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:98530400-98542000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:98530800-98542600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:98532400-98541200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:98532400-98546200	Weak transcription	Esophagus	oesophagus
43	chr3:98532600-98535800	Weak transcription	HepG2	liver
44	chr3:98532600-98537400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:98532800-98541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:98533200-98536600	Strong transcription	Fetal Kidney	kidney
47	chr3:98533200-98536800	Weak transcription	Liver	Liver
48	chr3:98533200-98538600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:98533400-98536200	Strong transcription	Fetal Lung	lung
50	chr3:98533600-98536000	Genic enhancers	NH-A	brain

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