Variant report

Variant	rs12063816
Chromosome Location	chr1:228408094-228408095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228405795..228408682-chr1:228408698..228410594,4	K562	blood:
2	chr1:228399642..228402754-chr1:228404803..228408505,4	MCF-7	breast:
3	chr1:228407306..228411999-chr1:228412295..228415050,4	K562	blood:
4	chr1:228399888..228402067-chr1:228407372..228409919,2	MCF-7	breast:
5	chr1:228390548..228393233-chr1:228405231..228408783,3	K562	blood:
6	chr1:228407306..228411999-chr1:228412295..228416286,6	K562	blood:

Variant related genes	Relation type
ENSG00000162913	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10157526	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10916279	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10916280	0.96[ASN][1000 genomes]
rs10916281	0.95[YRI][hapmap];0.98[AFR][1000 genomes]
rs12066906	0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60964166	0.89[AFR][1000 genomes]
rs6660457	0.99[AFR][1000 genomes]
rs6675092	0.81[CHB][hapmap]
rs6694419	0.80[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6694442	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
11	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228401400-228412200	Weak transcription	HSMMtube	muscle
2	chr1:228401400-228412600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:228401600-228412200	Weak transcription	Right Atrium	heart
4	chr1:228401800-228412000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:228402000-228412000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:228402000-228412200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:228402000-228412200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:228402000-228412600	Weak transcription	Fetal Kidney	kidney
9	chr1:228402200-228410200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:228402200-228411800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:228402200-228412200	Weak transcription	A549	lung
12	chr1:228402200-228412200	Weak transcription	Hela-S3	cervix
13	chr1:228402200-228412200	Weak transcription	NHEK	skin
14	chr1:228402200-228412400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:228402200-228412600	Weak transcription	Primary B cells from cord blood	blood
16	chr1:228402200-228415200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:228402400-228408400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:228402400-228411400	Strong transcription	Fetal Intestine Small	intestine
21	chr1:228402400-228411600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:228402400-228412400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:228402400-228412600	Weak transcription	HMEC	breast
24	chr1:228402600-228408400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:228402600-228408400	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr1:228402600-228408600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:228402600-228409000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr1:228402600-228410600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
30	chr1:228402800-228408200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:228402800-228408400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:228402800-228408800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:228402800-228409000	Strong transcription	Thymus	Thymus
34	chr1:228402800-228410400	Weak transcription	Fetal Lung	lung
35	chr1:228402800-228411800	Weak transcription	Esophagus	oesophagus
36	chr1:228402800-228412600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:228403000-228410200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:228403000-228412200	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:228403000-228412200	Weak transcription	Colonic Mucosa	Colon
40	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:228403200-228418000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:228403400-228408400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:228403400-228408400	Strong transcription	Fetal Brain Female	brain
44	chr1:228403400-228408600	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr1:228403400-228408600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:228403400-228415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:228403600-228408200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:228403600-228410600	Strong transcription	Dnd41	blood
49	chr1:228403800-228408200	Strong transcription	Fetal Thymus	thymus
50	chr1:228403800-228408600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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