Variant report

Variant	rs61340241
Chromosome Location	chr9:96332705-96332706
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	chr9:96332664-96332958	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:96332546-96333192	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:96331225..96334018-chr9:96347470..96349122,2	K562	blood:
2	chr9:96210381..96218248-chr9:96327402..96333234,10	MCF-7	breast:
3	chr9:96327412..96330304-chr9:96331068..96333359,2	K562	blood:
4	chr9:96205732..96207366-chr9:96330397..96333362,2	MCF-7	breast:
5	chr9:96212587..96215325-chr9:96332494..96334565,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263875	TF binding region
ENSG00000263875	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10046907	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124517	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512224	0.86[EUR][1000 genomes]
rs10512226	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12552189	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12553275	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1331588	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16909211	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28403269	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3897285	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4573340	0.90[EUR][1000 genomes]
rs4743916	0.81[EUR][1000 genomes]
rs4743920	0.81[EUR][1000 genomes]
rs4744229	0.81[EUR][1000 genomes]
rs55649770	0.89[EUR][1000 genomes]
rs55702483	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55812345	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55934002	0.81[EUR][1000 genomes]
rs56375911	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57303681	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57631285	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58782393	0.81[EUR][1000 genomes]
rs58790127	0.90[EUR][1000 genomes]
rs60212988	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60253984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60610533	0.83[ASN][1000 genomes]
rs60650773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479479	0.81[EUR][1000 genomes]
rs7020195	0.90[EUR][1000 genomes]
rs7038564	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651204	0.85[EUR][1000 genomes]
rs73651206	0.90[EUR][1000 genomes]
rs73651227	0.90[EUR][1000 genomes]
rs73651228	0.90[EUR][1000 genomes]
rs73651229	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73651232	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73651246	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73651248	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7854217	0.90[EUR][1000 genomes]
rs7854349	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7861929	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7874126	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs999326	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96329800-96333000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:96330000-96333000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:96330000-96333200	Weak transcription	A549	lung
4	chr9:96330000-96337200	Weak transcription	NHLF	lung
5	chr9:96330000-96337400	Weak transcription	Hela-S3	cervix
6	chr9:96330000-96337400	Weak transcription	HSMM	muscle
7	chr9:96330200-96332800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:96330200-96332800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:96330200-96332800	Weak transcription	Fetal Brain Female	brain
10	chr9:96330200-96333000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:96330200-96333000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:96330200-96333200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:96330200-96333200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:96330200-96333800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:96330200-96335200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:96330200-96335200	Weak transcription	Left Ventricle	heart
17	chr9:96330200-96335600	Weak transcription	Esophagus	oesophagus
18	chr9:96330200-96336400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:96330200-96336400	Weak transcription	Brain Substantia Nigra	brain
20	chr9:96330200-96336600	Weak transcription	Primary T cells from cord blood	blood
21	chr9:96330200-96336600	Weak transcription	Lung	lung
22	chr9:96330200-96336800	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:96330200-96336800	Weak transcription	Fetal Lung	lung
24	chr9:96330200-96337000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr9:96330200-96337000	Weak transcription	Fetal Intestine Small	intestine
26	chr9:96330200-96337000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:96330200-96337200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:96330200-96337200	Weak transcription	Aorta	Aorta
29	chr9:96330200-96337200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:96330200-96337200	Weak transcription	Colonic Mucosa	Colon
31	chr9:96330200-96337200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:96330200-96337200	Weak transcription	Osteobl	bone
33	chr9:96330200-96337400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:96330200-96337400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:96330200-96337400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:96330200-96337400	Weak transcription	Psoas Muscle	Psoas
37	chr9:96330200-96337400	Weak transcription	NHEK	skin
38	chr9:96330200-96337600	Weak transcription	Right Atrium	heart
39	chr9:96330400-96337000	Weak transcription	Fetal Heart	heart
40	chr9:96330800-96337200	Weak transcription	Pancreas	Pancrea
41	chr9:96331000-96334800	Weak transcription	Fetal Thymus	thymus
42	chr9:96331000-96335800	Weak transcription	Placenta	Placenta
43	chr9:96331000-96336800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr9:96331000-96336800	Weak transcription	Gastric	stomach
45	chr9:96331000-96336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr9:96331000-96337000	Weak transcription	Fetal Stomach	stomach
47	chr9:96331800-96333600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:96332000-96332800	Strong transcription	Fetal Muscle Leg	muscle
49	chr9:96332000-96333200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:96332000-96333600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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