Variant report

Variant	rs996226
Chromosome Location	chr1:227843790-227843791
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227842682..227845099-chr1:227847635..227850326,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12563117	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12563564	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12564736	1.00[EUR][1000 genomes]
rs12564917	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12564929	1.00[EUR][1000 genomes]
rs12565099	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12565109	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12565618	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12565653	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12566390	1.00[EUR][1000 genomes]
rs12566716	1.00[EUR][1000 genomes]
rs12566948	1.00[CHB][hapmap]
rs12567084	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12567160	1.00[EUR][1000 genomes]
rs12567934	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568707	1.00[EUR][1000 genomes]
rs1323021	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13373816	1.00[EUR][1000 genomes]
rs16841323	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16847912	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16847926	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16847929	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16847948	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16847987	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16848026	1.00[EUR][1000 genomes]
rs16848044	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848160	1.00[EUR][1000 genomes]
rs16859962	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16860227	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17492440	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17492447	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2101862	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2313220	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34984248	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35703429	1.00[EUR][1000 genomes]
rs4462138	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59461077	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6665512	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73090936	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73090937	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73090938	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73090948	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73090952	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73090954	0.81[ASN][1000 genomes]
rs73090985	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73090986	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73090987	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73090994	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73091000	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73092607	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73092610	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7554851	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7554870	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227820600-227861600	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr1:227827800-227845400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
4	chr1:227829400-227859800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:227830800-227845200	ZNF genes & repeats	Dnd41	blood
6	chr1:227831800-227850200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
7	chr1:227831800-227851600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:227831800-227854600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr1:227831800-227864000	ZNF genes & repeats	Liver	Liver
10	chr1:227832000-227845200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
11	chr1:227832000-227850200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr1:227832000-227854400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr1:227832200-227850600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:227832400-227850400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
15	chr1:227832600-227846400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
16	chr1:227833400-227849600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
17	chr1:227834000-227843800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr1:227834000-227847200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:227835000-227852200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:227835000-227852600	ZNF genes & repeats	Fetal Brain Female	brain
21	chr1:227835200-227845200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
22	chr1:227835200-227847800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
23	chr1:227836400-227852200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
24	chr1:227837000-227845000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
25	chr1:227838400-227846600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:227838600-227843800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:227838600-227845400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:227838600-227845400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
29	chr1:227838600-227847200	ZNF genes & repeats	Brain Substantia Nigra	brain
30	chr1:227838600-227849800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:227838600-227854400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:227838800-227849800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
33	chr1:227839600-227844200	Weak transcription	Esophagus	oesophagus
34	chr1:227839600-227847000	Weak transcription	Pancreas	Pancrea
35	chr1:227840600-227845400	ZNF genes & repeats	Fetal Lung	lung
36	chr1:227841200-227843800	ZNF genes & repeats	Brain Germinal Matrix	brain
37	chr1:227841200-227844000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:227841200-227852000	ZNF genes & repeats	Primary B cells from cord blood	blood
39	chr1:227841200-227852600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr1:227841200-227852800	ZNF genes & repeats	Brain Anterior Caudate	brain
41	chr1:227841400-227846400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:227841600-227852600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
43	chr1:227841800-227844600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr1:227842000-227844800	ZNF genes & repeats	Fetal Kidney	kidney
45	chr1:227842000-227845000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:227842000-227846400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
47	chr1:227842200-227844600	Weak transcription	Lung	lung
48	chr1:227842800-227845800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:227843000-227844600	Weak transcription	Right Atrium	heart
50	chr1:227843000-227846000	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links