Variant report

Variant	rs12146104
Chromosome Location	chr1:78448300-78448301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78447431..78449969-chr1:78468449..78471656,4	MCF-7	breast:
2	chr1:78447842..78450094-chr1:78543814..78546165,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAJB4-1	chr1:78444779-78456066	NONHSAT004062

Variant related genes	Relation type
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10437022	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10873960	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11162400	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11162403	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1166697	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1166701	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1166702	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1166704	0.84[AMR][1000 genomes]
rs1166705	0.87[AMR][1000 genomes]
rs1166706	0.87[AMR][1000 genomes]
rs1166707	0.90[AMR][1000 genomes]
rs11805735	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11807240	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12405212	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12409561	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12723748	0.84[AMR][1000 genomes]
rs1335481	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1536160	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1555798	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1616949	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17383213	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17387365	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1971368	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2136682	0.83[EUR][1000 genomes]
rs2274257	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2296453	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3767028	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4370803	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4372306	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949828	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4949829	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57421725	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6424640	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6424650	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6424660	0.82[AMR][1000 genomes]
rs6656888	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs750720	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7514007	0.81[AMR][1000 genomes]
rs7538210	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9324166	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9659938	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9661193	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9730688	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78445800-78449600	Weak transcription	Stomach Mucosa	stomach
2	chr1:78445800-78449800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:78446000-78449800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:78446000-78449800	Weak transcription	Small Intestine	intestine
5	chr1:78446000-78451800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr1:78446000-78452600	Weak transcription	Gastric	stomach
7	chr1:78446000-78455600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:78446000-78458600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:78446000-78458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:78446000-78461000	Weak transcription	Placenta	Placenta
11	chr1:78446200-78448400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:78446200-78449400	Weak transcription	Fetal Intestine Large	intestine
13	chr1:78446200-78451800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:78446200-78452400	Weak transcription	Psoas Muscle	Psoas
15	chr1:78446200-78452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:78446200-78457200	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:78446200-78461200	Weak transcription	Fetal Stomach	stomach
18	chr1:78446200-78469600	Weak transcription	Thymus	Thymus
19	chr1:78446400-78451800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:78446400-78458200	Weak transcription	Fetal Thymus	thymus
21	chr1:78446400-78469800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:78446400-78470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:78446600-78449400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:78446600-78449600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:78446600-78449600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:78446600-78449600	Weak transcription	Fetal Intestine Small	intestine
27	chr1:78446600-78449600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:78446600-78449800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:78446600-78450000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:78446600-78450000	Weak transcription	Fetal Heart	heart
31	chr1:78446600-78450600	Weak transcription	HSMMtube	muscle
32	chr1:78446600-78450800	Weak transcription	Primary B cells from cord blood	blood
33	chr1:78446600-78450800	Enhancers	HepG2	liver
34	chr1:78446600-78451800	Weak transcription	Right Atrium	heart
35	chr1:78446600-78457200	Weak transcription	Primary T cells from cord blood	blood
36	chr1:78446600-78459200	Weak transcription	Fetal Brain Female	brain
37	chr1:78446600-78460800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:78446600-78461200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:78446600-78468000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:78446600-78468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:78446600-78468800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:78446600-78468800	Weak transcription	Adipose Nuclei	Adipose
43	chr1:78446600-78468800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:78446600-78469000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:78446600-78469000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:78446600-78469000	Weak transcription	Fetal Kidney	kidney
47	chr1:78446600-78469600	Weak transcription	Aorta	Aorta
48	chr1:78446600-78469800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:78446600-78470200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:78446600-78470400	Weak transcription	H9 Cell Line	embryonic stem cell

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