Variant report

Variant	rs3136331
Chromosome Location	chr2:48025172-48025173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48011141..48015679-chr2:48023292..48025475,4	MCF-7	breast:
2	chr2:48024799..48028415-chr2:48033995..48037320,3	K562	blood:
3	chr2:48008730..48016091-chr2:48023378..48031018,13	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNK12-4	chr2:48024965-48025230	NONHSAT070599

Variant related genes	Relation type
ENSG00000116062	Chromatin interaction
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11682547	1.00[AFR][1000 genomes]
rs1800931	1.00[AFR][1000 genomes]
rs3136271	1.00[EUR][1000 genomes]
rs56320267	1.00[AFR][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	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats 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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48011800-48026200	Weak transcription	Stomach Mucosa	stomach
2	chr2:48012000-48026000	Weak transcription	Esophagus	oesophagus
3	chr2:48012000-48026000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:48012000-48026200	Weak transcription	Gastric	stomach
5	chr2:48012200-48026000	Weak transcription	Small Intestine	intestine
6	chr2:48012200-48030000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:48013400-48025800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:48015000-48029600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:48016000-48029600	Strong transcription	Fetal Thymus	thymus
11	chr2:48016200-48029600	Strong transcription	Fetal Stomach	stomach
12	chr2:48016200-48030000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:48016200-48050400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:48016400-48029800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:48016600-48025800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:48016600-48030000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:48016800-48030200	Strong transcription	Fetal Muscle Leg	muscle
18	chr2:48017000-48036200	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr2:48017000-48049400	Strong transcription	Fetal Intestine Large	intestine
20	chr2:48017200-48025800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:48017200-48053200	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:48017400-48032200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:48017400-48049600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr2:48017800-48037800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:48018000-48025800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:48018000-48030200	Strong transcription	Brain Germinal Matrix	brain
27	chr2:48018000-48030400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:48018200-48030200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:48018200-48030200	Strong transcription	Fetal Brain Female	brain
30	chr2:48018200-48030600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:48018400-48029200	Strong transcription	A549	lung
32	chr2:48018400-48030200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr2:48018600-48026600	Strong transcription	Fetal Intestine Small	intestine
34	chr2:48018600-48027400	Weak transcription	Psoas Muscle	Psoas
35	chr2:48018600-48030200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:48019600-48030600	Strong transcription	Liver	Liver
37	chr2:48019800-48026600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:48020800-48030200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:48020800-48030400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:48021000-48029800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:48021200-48029000	Strong transcription	HMEC	breast
42	chr2:48021200-48030400	Strong transcription	Fetal Lung	lung
43	chr2:48021200-48036200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:48021200-48036400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:48021200-48051600	Strong transcription	Placenta	Placenta
46	chr2:48021400-48030000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:48021400-48030000	Strong transcription	GM12878-XiMat	blood
48	chr2:48021400-48030200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:48021400-48030200	Strong transcription	Fetal Kidney	kidney
50	chr2:48021400-48030200	Strong transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links