Variant report

Variant	rs7980639
Chromosome Location	chr12:51472210-51472211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr12:51471706-51472309	U2OS	brain:	n/a	n/a
2	GATA3	chr12:51472016-51472474	MCF-7	breast:	n/a	n/a
3	GATA3	chr12:51472130-51472439	T-47D	breast:	n/a	n/a
4	GATA3	chr12:51471923-51472487	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr12:51471701-51472276	MCF-7	breast:	n/a	n/a
6	GATA3	chr12:51472107-51472380	MCF-7	breast:	n/a	n/a
7	GATA3	chr12:51471994-51472509	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51470174..51472582-chr12:51632362..51634494,2	K562	blood:
2	chr12:51468579..51474515-chr12:51475298..51478642,16	K562	blood:

Variant related genes	Relation type
CSRNP2	TF binding region
ENSG00000110925	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10735830	0.82[AFR][1000 genomes]
rs2436649	0.87[AFR][1000 genomes]
rs2640508	0.84[AFR][1000 genomes]
rs2640517	0.84[AFR][1000 genomes]
rs2640519	0.84[AFR][1000 genomes]
rs2640524	0.82[AFR][1000 genomes]
rs2640529	0.80[AFR][1000 genomes]
rs4238109	0.88[AFR][1000 genomes]
rs4768966	0.82[AFR][1000 genomes]
rs6580786	0.95[AFR][1000 genomes]
rs7968372	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51443400-51476000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:51454000-51475400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:51454200-51475600	Weak transcription	Stomach Mucosa	stomach
4	chr12:51459000-51475600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:51459800-51475800	Weak transcription	GM12878-XiMat	blood
6	chr12:51461800-51475200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:51462000-51475800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:51462000-51475800	Weak transcription	Pancreas	Pancrea
9	chr12:51462000-51476400	Weak transcription	Gastric	stomach
10	chr12:51462600-51474400	Weak transcription	Fetal Kidney	kidney
11	chr12:51464400-51475800	Weak transcription	HMEC	breast
12	chr12:51464800-51475800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:51466000-51475400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:51466000-51475400	Weak transcription	A549	lung
15	chr12:51466400-51475600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:51466800-51475800	Weak transcription	Hela-S3	cervix
17	chr12:51467200-51475600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:51467200-51475800	Weak transcription	Primary B cells from cord blood	blood
19	chr12:51467400-51476200	Weak transcription	Colonic Mucosa	Colon
20	chr12:51467800-51473600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:51467800-51475200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:51467800-51475200	Weak transcription	HUVEC	blood vessel
23	chr12:51467800-51475400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:51467800-51475400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:51467800-51475800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:51467800-51475800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr12:51467800-51475800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr12:51467800-51475800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:51467800-51475800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:51467800-51475800	Weak transcription	Liver	Liver
31	chr12:51468000-51475600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:51468000-51475600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:51468000-51476000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:51468000-51476400	Weak transcription	Esophagus	oesophagus
35	chr12:51468200-51476000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:51468400-51475200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:51468400-51475200	Weak transcription	Fetal Lung	lung
38	chr12:51468400-51475200	Weak transcription	NHLF	lung
39	chr12:51468400-51475600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:51468400-51475800	Weak transcription	Fetal Intestine Large	intestine
41	chr12:51468400-51476000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:51469000-51472400	Enhancers	Brain Hippocampus Middle	brain
43	chr12:51469600-51475800	Weak transcription	Spleen	Spleen
44	chr12:51470000-51475800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:51470200-51475600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:51470200-51475800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:51470200-51475800	Weak transcription	Small Intestine	intestine
48	chr12:51470200-51475800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr12:51470400-51475400	Weak transcription	Fetal Stomach	stomach
50	chr12:51470400-51475800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links