Variant report

Variant	rs7540096
Chromosome Location	chr1:161721351-161721352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:
2	chr1:161703503..161707776-chr1:161717836..161724077,7	K562	blood:
3	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
4	chr1:161696672..161698764-chr1:161719597..161721628,3	K562	blood:
5	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
6	chr1:161719690..161721736-chr1:161980982..161982945,2	MCF-7	breast:
7	chr1:161704696..161707209-chr1:161718366..161721899,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241347	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000226889	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1027701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1027702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12026445	0.88[CHB][hapmap]
rs12116756	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12121522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12564653	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1417580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2174208	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4656332	0.81[EUR][1000 genomes]
rs4657096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4657097	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4657098	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6427624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6427625	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS 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	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161720400-161721600	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr1:161720400-161734600	Weak transcription	Aorta	Aorta
3	chr1:161720600-161721400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:161720600-161721600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:161720600-161721600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:161720600-161721600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:161720600-161722000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:161720600-161722400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:161720600-161724200	Weak transcription	Esophagus	oesophagus
10	chr1:161720600-161728800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:161720600-161734600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:161720600-161734800	Weak transcription	Psoas Muscle	Psoas
13	chr1:161720600-161736000	Weak transcription	Spleen	Spleen
14	chr1:161720800-161721400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:161720800-161721400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:161720800-161721400	Weak transcription	Primary T cells from cord blood	blood
17	chr1:161720800-161721400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:161720800-161721400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:161720800-161721400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:161720800-161721400	Weak transcription	Fetal Thymus	thymus
21	chr1:161720800-161721400	Weak transcription	HSMM	muscle
22	chr1:161720800-161721400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:161720800-161721600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:161720800-161721600	Weak transcription	Adipose Nuclei	Adipose
25	chr1:161720800-161721600	Weak transcription	Brain Anterior Caudate	brain
26	chr1:161720800-161721600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:161720800-161721800	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:161720800-161722400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:161720800-161734600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:161720800-161735000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:161720800-161735000	Weak transcription	Stomach Mucosa	stomach
32	chr1:161721000-161721400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:161721000-161721400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:161721000-161721400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:161721000-161721400	Genic enhancers	HUVEC	blood vessel
36	chr1:161721000-161721400	Transcr. at gene 5' and 3'	NH-A	brain
37	chr1:161721000-161721400	Weak transcription	Osteobl	bone
38	chr1:161721000-161721600	Genic enhancers	Primary hematopoietic stem cells	blood
39	chr1:161721000-161721600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:161721000-161721600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:161721000-161721600	Weak transcription	Fetal Kidney	kidney
42	chr1:161721000-161721600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:161721000-161721600	Weak transcription	NHDF-Ad	bronchial
44	chr1:161721000-161721800	Weak transcription	Brain Angular Gyrus	brain
45	chr1:161721000-161722000	Enhancers	Fetal Brain Male	brain
46	chr1:161721000-161723600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:161721000-161726800	Strong transcription	Fetal Lung	lung
48	chr1:161721000-161728200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:161721000-161728800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:161721000-161728800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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