Variant report

Variant	rs4742131
Chromosome Location	chr9:5881193-5881194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:5880522..5882906-chr9:5883810..5886379,2	K562	blood:
2	chr9:5870831..5873725-chr9:5878360..5881340,2	K562	blood:
3	chr9:5828344..5834722-chr9:5880387..5886482,7	MCF-7	breast:
4	chr9:5839459..5843654-chr9:5878363..5884455,6	MCF-7	breast:
5	chr9:5864598..5866719-chr9:5878064..5881327,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099219	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10121480	1.00[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes]
rs10733517	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs10733520	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs10739079	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs10758731	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs10758732	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs10758734	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs10815330	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs10815335	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap]
rs1260130	1.00[TSI][hapmap]
rs1331378	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1331379	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs1418740	1.00[CEU][hapmap]
rs1478937	0.85[JPT][hapmap]
rs1478938	1.00[JPT][hapmap]
rs16923551	1.00[ASW][hapmap]
rs16923578	1.00[CEU][hapmap]
rs1776008	1.00[TSI][hapmap]
rs186913	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs1888703	0.81[JPT][hapmap]
rs2150703	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2244053	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2244058	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291055	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2381360	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2797512	1.00[TSI][hapmap]
rs2797519	1.00[TSI][hapmap]
rs343469	1.00[CEU][hapmap]
rs343471	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs343480	1.00[CEU][hapmap]
rs343482	1.00[CEU][hapmap]
rs343500	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs3739649	1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs4075225	1.00[CEU][hapmap]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs4395943	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap]
rs4740833	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs6477017	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6477024	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs7019606	1.00[CEU][hapmap]
rs7021498	1.00[CEU][hapmap]
rs7024130	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs7026454	0.83[JPT][hapmap]
rs7029833	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs7030731	1.00[CEU][hapmap]
rs7032130	1.00[CEU][hapmap]
rs7034210	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs7037680	1.00[TSI][hapmap]
rs7042947	1.00[CEU][hapmap]
rs7044750	1.00[CEU][hapmap]
rs7864247	0.87[ASN][1000 genomes]
rs7866793	1.00[CEU][hapmap]
rs7868062	1.00[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1033546	chr9:5875201-5900427	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5834400-5886000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:5840400-5921600	Weak transcription	Right Ventricle	heart
3	chr9:5852200-5897000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr9:5853800-5895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:5854400-5886200	Weak transcription	Brain Anterior Caudate	brain
6	chr9:5856800-5895600	Weak transcription	Brain Substantia Nigra	brain
7	chr9:5858600-5885800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:5859000-5895600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:5859000-5906600	Weak transcription	Ovary	ovary
10	chr9:5859200-5919800	Weak transcription	Fetal Brain Female	brain
11	chr9:5863400-5895600	Weak transcription	Fetal Intestine Small	intestine
12	chr9:5863600-5896600	Weak transcription	Pancreas	Pancrea
13	chr9:5864800-5881400	Weak transcription	Spleen	Spleen
14	chr9:5864800-5895600	Weak transcription	Gastric	stomach
15	chr9:5865200-5886000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:5870000-5886400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:5870800-5895600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:5871000-5895600	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:5871000-5920000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:5871200-5898400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:5875600-5881600	Weak transcription	Primary T cells from cord blood	blood
22	chr9:5875600-5884800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:5876000-5885000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:5876800-5886000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:5877000-5895600	Weak transcription	Left Ventricle	heart
26	chr9:5877000-5896000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:5877200-5886200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:5877200-5886200	Weak transcription	Brain Angular Gyrus	brain
29	chr9:5877200-5894200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:5877200-5895400	Weak transcription	Fetal Stomach	stomach
31	chr9:5877200-5895600	Weak transcription	Aorta	Aorta
32	chr9:5879000-5881600	Enhancers	Placenta	Placenta
33	chr9:5879600-5882000	Enhancers	K562	blood
34	chr9:5880000-5881400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:5880000-5886000	Weak transcription	A549	lung
36	chr9:5880200-5881200	Enhancers	Hela-S3	cervix
37	chr9:5880200-5884400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:5880400-5883400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:5880400-5883800	Weak transcription	NHEK	skin
40	chr9:5880400-5884200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:5880600-5883800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:5880600-5884000	Weak transcription	HMEC	breast
43	chr9:5880600-5884400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:5880600-5887200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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