Variant report

Variant	rs13301956
Chromosome Location	chr9:86271927-86271928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86271855..86273661-chr9:86280180..86281686,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10114717	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115073	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10116424	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121045	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121882	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122131	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122134	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123002	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124333	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125987	0.85[CEU][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044214	0.83[YRI][hapmap]
rs10481738	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140184	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140193	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140196	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140201	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140213	0.86[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12335711	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340935	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342901	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343837	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344615	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345514	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351677	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289229	1.00[ASN][1000 genomes]
rs13291631	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13292088	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13294533	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780983	1.00[ASN][1000 genomes]
rs2780987	1.00[ASN][1000 genomes]
rs2780988	1.00[ASN][1000 genomes]
rs2780989	1.00[ASN][1000 genomes]
rs2781002	0.82[YRI][hapmap]
rs2781006	0.82[YRI][hapmap]
rs2811898	1.00[ASN][1000 genomes]
rs28555298	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3447	1.00[ASN][1000 genomes]
rs34778713	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34891935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35378833	1.00[ASN][1000 genomes]
rs35535452	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364707	1.00[ASN][1000 genomes]
rs7045761	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944947	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987871	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers 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
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86239600-86272200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:86244800-86278800	Weak transcription	Spleen	Spleen
3	chr9:86244800-86285800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:86252800-86294000	Weak transcription	Small Intestine	intestine
5	chr9:86258800-86272600	Weak transcription	Stomach Mucosa	stomach
6	chr9:86260600-86300400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:86260800-86281400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:86261000-86280200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:86262800-86272000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:86263400-86298800	Strong transcription	Fetal Thymus	thymus
11	chr9:86264400-86280200	Strong transcription	Fetal Muscle Leg	muscle
12	chr9:86264600-86280200	Strong transcription	Adipose Nuclei	Adipose
13	chr9:86264600-86280400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr9:86264600-86280600	Strong transcription	Stomach Smooth Muscle	stomach
15	chr9:86264600-86281400	Strong transcription	HSMMtube	muscle
16	chr9:86264600-86284200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:86264600-86284400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:86264600-86297000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr9:86264800-86279400	Strong transcription	Primary T cells from cord blood	blood
20	chr9:86264800-86280200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr9:86264800-86280200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr9:86264800-86280200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr9:86264800-86281800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:86264800-86294600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:86264800-86295600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:86264800-86298200	Strong transcription	Dnd41	blood
27	chr9:86264800-86300200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:86265000-86274000	Strong transcription	Fetal Intestine Large	intestine
29	chr9:86265000-86280000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:86265000-86280800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr9:86265000-86282000	Strong transcription	Placenta	Placenta
32	chr9:86265000-86284400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:86265000-86295200	Strong transcription	HSMM	muscle
34	chr9:86265000-86296800	Strong transcription	Liver	Liver
35	chr9:86265000-86298800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr9:86265200-86281400	Strong transcription	NH-A	brain
37	chr9:86265400-86274600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr9:86265400-86285800	Weak transcription	Gastric	stomach
39	chr9:86265600-86273200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr9:86265600-86277600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:86266000-86281600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:86266000-86283600	Strong transcription	NHDF-Ad	bronchial
43	chr9:86266200-86280600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr9:86266200-86296000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr9:86266400-86279800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:86266400-86281800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:86266400-86298800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr9:86266600-86272000	Weak transcription	Aorta	Aorta
49	chr9:86267000-86274400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr9:86267000-86277600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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