Variant report

Variant	rs2296707
Chromosome Location	chr9:97401786-97401787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96927010..96929542-chr9:97400485..97402088,2	MCF-7	breast:
2	chr9:97399286..97401961-chr9:97487355..97490023,2	MCF-7	breast:
3	chr9:97316754..97318987-chr9:97400777..97403144,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBP1-1	chr9:97401648-97401788	NONHSAT133331

Variant related genes	Relation type
ENSG00000231806	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000269946	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10993270	0.85[CHB][hapmap]
rs12006206	0.81[CHB][hapmap]
rs12683407	0.81[EUR][1000 genomes]
rs12684841	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12684849	0.81[EUR][1000 genomes]
rs12685485	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16910850	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16910853	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16910860	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28369691	0.90[EUR][1000 genomes]
rs28369738	0.81[EUR][1000 genomes]
rs28369782	0.81[EUR][1000 genomes]
rs28369786	0.81[EUR][1000 genomes]
rs28402377	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402378	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402384	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402386	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402389	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402390	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402396	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28402397	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28402401	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28402404	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4111369	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4129219	0.81[CHB][hapmap]
rs4574908	0.82[JPT][hapmap]
rs59327242	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59727084	0.81[EUR][1000 genomes]
rs7019207	0.85[CEU][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7028990	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7035325	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73523269	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73523271	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7849320	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850385	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7859022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867069	0.80[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv614918	chr9:97380597-97412037	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv893597	chr9:97380597-97463435	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97400200-97402200	Active TSS	Liver	Liver
2	chr9:97400400-97401800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr9:97400400-97402000	Active TSS	Stomach Mucosa	stomach
4	chr9:97400600-97402200	Bivalent/Poised TSS	Fetal Kidney	kidney
5	chr9:97400600-97402200	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr9:97400600-97402400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:97400800-97401800	Flanking Active TSS	Right Ventricle	heart
8	chr9:97400800-97402200	Active TSS	Gastric	stomach
9	chr9:97401000-97401800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:97401000-97401800	Flanking Active TSS	Esophagus	oesophagus
11	chr9:97401000-97401800	Flanking Active TSS	Lung	lung
12	chr9:97401000-97402000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr9:97401000-97402200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
14	chr9:97401000-97402400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr9:97401000-97402400	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr9:97401000-97402400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:97401000-97402400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr9:97401000-97402400	Active TSS	Right Atrium	heart
19	chr9:97401000-97402600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr9:97401000-97402600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr9:97401000-97402600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:97401000-97402600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:97401000-97402600	Active TSS	Rectal Smooth Muscle	rectum
24	chr9:97401000-97402800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr9:97401000-97402800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr9:97401000-97403000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr9:97401200-97401800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
28	chr9:97401200-97401800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:97401200-97401800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:97401200-97401800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:97401200-97401800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
32	chr9:97401200-97401800	Flanking Bivalent TSS/Enh	Left Ventricle	heart
33	chr9:97401200-97401800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
34	chr9:97401200-97402000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
35	chr9:97401200-97402200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:97401200-97402200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
37	chr9:97401200-97402200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:97401200-97402200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:97401200-97402200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:97401200-97402200	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr9:97401200-97402200	Active TSS	Small Intestine	intestine
42	chr9:97401200-97402400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr9:97401200-97402400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:97401200-97402400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr9:97401200-97402400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr9:97401200-97402400	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr9:97401200-97402600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:97401200-97402600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
49	chr9:97401400-97401800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:97401400-97401800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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