Variant report

Variant	rs9824430
Chromosome Location	chr3:99809372-99809373
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99796671..99799694-chr3:99807406..99810771,4	K562	blood:
2	chr3:99808255..99810946-chr3:99815200..99817983,2	MCF-7	breast:
3	chr3:99536338..99538401-chr3:99807558..99809928,2	K562	blood:
4	chr3:99807984..99809965-chr3:99822463..99825380,2	MCF-7	breast:
5	chr3:99809166..99811097-chr3:99816602..99818657,2	K562	blood:
6	chr3:99807438..99810251-chr3:99824386..99825972,2	K562	blood:
7	chr3:99796671..99799492-chr3:99807406..99809668,2	K562	blood:

Variant related genes	Relation type
ENSG00000184220	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12486901	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12487143	0.81[CEU][hapmap]
rs12489030	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12494994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496041	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1387649	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1565341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928233	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4928236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928240	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6414382	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6777622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792339	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6800456	0.88[JPT][hapmap]
rs73859922	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7632345	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7634628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7641782	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs7652706	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9827744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9872339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99793800-99809800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99805000-99809600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr3:99806200-99809800	Enhancers	NHDF-Ad	bronchial
5	chr3:99806200-99816000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:99806200-99818600	Weak transcription	HSMM	muscle
7	chr3:99806600-99812600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:99806800-99809400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:99806800-99809600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:99806800-99809800	Enhancers	HepG2	liver
11	chr3:99807000-99809800	Enhancers	H1 Cell Line	embryonic stem cell
12	chr3:99807000-99809800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:99807200-99809600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:99807400-99809400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:99807400-99809400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:99807400-99810600	Enhancers	A549	lung
17	chr3:99807600-99809600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:99807800-99809400	Weak transcription	Liver	Liver
19	chr3:99807800-99810400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr3:99808000-99809400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:99808000-99809600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:99808000-99809600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr3:99808400-99809400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:99808400-99809400	Flanking Active TSS	K562	blood
25	chr3:99808400-99809800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:99808400-99809800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:99808400-99809800	Enhancers	Osteobl	bone
28	chr3:99808600-99809400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:99808600-99809400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:99808600-99809600	Enhancers	Ovary	ovary
31	chr3:99808600-99809800	Enhancers	Adipose Nuclei	Adipose
32	chr3:99808600-99809800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:99808600-99809800	Enhancers	Fetal Kidney	kidney
34	chr3:99808600-99809800	Enhancers	Psoas Muscle	Psoas
35	chr3:99808600-99809800	Enhancers	NH-A	brain
36	chr3:99808600-99809800	Enhancers	NHLF	lung
37	chr3:99808800-99809600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:99808800-99809600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:99808800-99809600	Enhancers	Fetal Intestine Large	intestine
40	chr3:99808800-99809600	Enhancers	Fetal Intestine Small	intestine
41	chr3:99808800-99809600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr3:99808800-99809600	Enhancers	Small Intestine	intestine
43	chr3:99808800-99809600	Enhancers	HMEC	breast
44	chr3:99808800-99809800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:99808800-99809800	Enhancers	Fetal Muscle Leg	muscle
46	chr3:99808800-99809800	Enhancers	Placenta	Placenta
47	chr3:99808800-99809800	Enhancers	Left Ventricle	heart
48	chr3:99808800-99809800	Enhancers	GM12878-XiMat	blood
49	chr3:99808800-99809800	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr3:99808800-99810000	Enhancers	Fetal Lung	lung

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