Variant report

Variant	rs1871220
Chromosome Location	chr9:97819743-97819744
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	chr9:97819371..97821085-chr9:97852918..97854464,2	MCF-7	breast:
2	chr9:97809147..97811872-chr9:97817665..97820103,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1020962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217441	1.00[CEU][hapmap]
rs1038092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732407	1.00[CEU][hapmap]
rs10761362	1.00[CEU][hapmap]
rs10761371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12555128	1.00[JPT][hapmap]
rs12555829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1542108	1.00[CEU][hapmap]
rs1564235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571897	0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs16911834	1.00[JPT][hapmap]
rs16911856	1.00[JPT][hapmap]
rs1699499	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1888944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888945	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888946	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061799	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2061801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104888	1.00[JPT][hapmap]
rs2306207	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs242448	1.00[JPT][hapmap]
rs356660	1.00[JPT][hapmap]
rs356661	1.00[JPT][hapmap]
rs356685	1.00[JPT][hapmap]
rs356686	1.00[JPT][hapmap]
rs3739748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780560	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4332191	1.00[CEU][hapmap]
rs4743972	1.00[CEU][hapmap]
rs4743975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743976	0.81[AMR][1000 genomes]
rs4743977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743989	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4744421	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744429	1.00[ASN][1000 genomes]
rs4744437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4744440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs475413	1.00[JPT][hapmap]
rs6479578	1.00[CEU][hapmap]
rs6479589	0.81[AMR][1000 genomes]
rs6479596	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479597	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67134693	0.96[ASN][1000 genomes]
rs7019602	1.00[CEU][hapmap]
rs7022739	0.81[AMR][1000 genomes]
rs7022963	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7023719	1.00[CEU][hapmap]
rs7025100	1.00[CEU][hapmap]
rs7039768	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs72750335	0.96[ASN][1000 genomes]
rs72750346	0.96[ASN][1000 genomes]
rs72750351	0.96[ASN][1000 genomes]
rs72750359	0.96[ASN][1000 genomes]
rs72750367	1.00[ASN][1000 genomes]
rs72750373	1.00[ASN][1000 genomes]
rs73540087	1.00[ASN][1000 genomes]
rs7867856	1.00[CEU][hapmap]
rs894426	1.00[CEU][hapmap]
rs9299427	0.83[ASN][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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97811400-97820800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:97813000-97820600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:97813000-97873000	Weak transcription	K562	blood
4	chr9:97813400-97827200	Genic enhancers	Liver	Liver
5	chr9:97815200-97824400	Weak transcription	Thymus	Thymus
6	chr9:97816000-97823000	Enhancers	Fetal Heart	heart
7	chr9:97816400-97820400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:97816400-97821600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:97816600-97820600	Enhancers	Fetal Kidney	kidney
10	chr9:97817200-97821000	Transcr. at gene 5' and 3'	A549	lung
11	chr9:97817400-97821200	Enhancers	Primary hematopoietic stem cells	blood
12	chr9:97817400-97821400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr9:97817400-97821600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr9:97817400-97821800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr9:97817600-97819800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr9:97817600-97819800	Flanking Active TSS	NH-A	brain
17	chr9:97817600-97819800	Flanking Active TSS	NHDF-Ad	bronchial
18	chr9:97817600-97820000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr9:97817600-97820000	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr9:97817600-97821000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:97817600-97821000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr9:97817600-97826000	Genic enhancers	HepG2	liver
23	chr9:97817600-97826400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:97817800-97819800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr9:97817800-97819800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:97817800-97819800	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr9:97817800-97820000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr9:97817800-97820800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:97817800-97820800	Flanking Active TSS	Fetal Stomach	stomach
30	chr9:97817800-97821200	Flanking Active TSS	NHLF	lung
31	chr9:97817800-97821400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr9:97817800-97821600	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr9:97817800-97821600	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr9:97818000-97819800	Active TSS	Colonic Mucosa	Colon
35	chr9:97818000-97819800	Transcr. at gene 5' and 3'	HSMM	muscle
36	chr9:97818000-97821200	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr9:97818000-97822800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:97818000-97824400	Weak transcription	GM12878-XiMat	blood
39	chr9:97818200-97819800	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr9:97818200-97823000	Enhancers	Stomach Mucosa	stomach
41	chr9:97818400-97820000	Flanking Active TSS	Fetal Lung	lung
42	chr9:97818400-97820200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
43	chr9:97818400-97825000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr9:97818600-97819800	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr9:97818600-97819800	Enhancers	HMEC	breast
46	chr9:97818600-97820000	Genic enhancers	NHEK	skin
47	chr9:97818800-97819800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr9:97818800-97819800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:97818800-97819800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr9:97818800-97820200	Enhancers	Pancreas	Pancrea

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