Variant report

Variant	rs16972779
Chromosome Location	chr15:42453963-42453964
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	chr15:42452722..42455427-chr15:42457119..42459983,4	K562	blood:
2	chr15:42453296..42455922-chr15:42565346..42568176,2	K562	blood:

Variant related genes	Relation type
ENSG00000214013	Chromatin interaction
ENSG00000166887	Chromatin interaction
ENSG00000103978	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10220859	0.85[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap]
rs12437600	0.88[AMR][1000 genomes]
rs12438509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12440087	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12441016	0.86[AMR][1000 genomes]
rs12441642	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs16972770	1.00[CHB][hapmap]
rs16972776	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap]
rs16972887	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973008	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16973045	1.00[CHB][hapmap]
rs16973060	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2138831	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2412688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs3736099	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3743005	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3743007	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3743008	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3825785	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4506867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs4923932	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4923945	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4924630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4924631	0.82[ASN][1000 genomes]
rs4924672	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4924673	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56030609	0.90[ASN][1000 genomes]
rs56914671	0.92[ASN][1000 genomes]
rs57393446	0.84[ASN][1000 genomes]
rs57976413	0.85[AMR][1000 genomes]
rs58179171	0.86[EUR][1000 genomes]
rs59893734	0.84[ASN][1000 genomes]
rs60443443	0.84[ASN][1000 genomes]
rs61069354	0.82[AMR][1000 genomes]
rs7180279	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7181979	0.84[ASN][1000 genomes]
rs73403365	0.82[AMR][1000 genomes]
rs73407403	0.84[ASN][1000 genomes]
rs73407407	0.84[ASN][1000 genomes]
rs73409577	0.85[AMR][1000 genomes]
rs8025601	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42449000-42481800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:42449200-42456000	Weak transcription	Stomach Mucosa	stomach
3	chr15:42449600-42468200	Strong transcription	Fetal Brain Female	brain
4	chr15:42450200-42468600	Strong transcription	Fetal Stomach	stomach
5	chr15:42450200-42472400	Strong transcription	Fetal Intestine Small	intestine
6	chr15:42450400-42457000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:42450400-42468400	Strong transcription	Primary T cells from cord blood	blood
8	chr15:42450400-42468400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr15:42450400-42476600	Strong transcription	Fetal Muscle Leg	muscle
10	chr15:42450600-42457400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:42450600-42460800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:42450600-42463400	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:42450600-42468000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:42450600-42468200	Strong transcription	Brain Germinal Matrix	brain
15	chr15:42450600-42479800	Weak transcription	Psoas Muscle	Psoas
16	chr15:42450600-42485000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:42450600-42486200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:42450600-42487400	Strong transcription	Primary B cells from cord blood	blood
19	chr15:42450800-42463400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:42450800-42471400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:42450800-42484000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:42450800-42485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:42450800-42485200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:42451000-42460800	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr15:42451000-42460800	Strong transcription	HepG2	liver
26	chr15:42451000-42461000	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr15:42451000-42461000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:42451000-42461200	Strong transcription	Gastric	stomach
29	chr15:42451000-42461200	Strong transcription	Spleen	Spleen
30	chr15:42451000-42462000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:42451000-42462000	Strong transcription	Colonic Mucosa	Colon
32	chr15:42451000-42462400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:42451000-42462600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr15:42451000-42463200	Strong transcription	Adipose Nuclei	Adipose
35	chr15:42451000-42463400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr15:42451000-42463400	Strong transcription	GM12878-XiMat	blood
37	chr15:42451000-42463600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:42451000-42466000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:42451000-42466000	Strong transcription	Colon Smooth Muscle	Colon
40	chr15:42451000-42466000	Strong transcription	Pancreas	Pancrea
41	chr15:42451000-42468600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:42451000-42471000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:42451000-42479600	Strong transcription	Liver	Liver
44	chr15:42451000-42484000	Strong transcription	Placenta	Placenta
45	chr15:42451000-42484400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:42451000-42484800	Strong transcription	Fetal Intestine Large	intestine
47	chr15:42451000-42484800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:42451000-42485000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:42451000-42485000	Strong transcription	Thymus	Thymus
50	chr15:42451000-42487600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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