Variant report

Variant	rs73094978
Chromosome Location	chr2:233940279-233940280
allele	A/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	POLR2A	chr2:233939495-233941193	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:233940180-233940625	GM12878	blood:	n/a	n/a
3	WRNIP1	chr2:233939366-233941159	GM12878	blood:	n/a	n/a
4	CHD1	chr2:233940190-233941710	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:233938359-233941839	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:233939995-233941232	GM12878	blood:	n/a	n/a
7	RCOR1	chr2:233940156-233941171	GM12878	blood:	n/a	n/a
8	POU2F2	chr2:233940174-233941183	GM12878	blood:	n/a	chr2:233940901-233940911 chr2:233940899-233940914 chr2:233940903-233940910 chr2:233940901-233940911 chr2:233940903-233940911 chr2:233940900-233940913 chr2:233940900-233940912 chr2:233940902-233940913 chr2:233940902-233940911 chr2:233940900-233940914 chr2:233940898-233940916 chr2:233940902-233940912
9	MTA3	chr2:233939964-233940502	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:233938464-233941811	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:233940028-233941150	GM12891	blood:	n/a	n/a
12	ELK1	chr2:233940080-233941819	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:233939505-233941200	GM12891	blood:	n/a	n/a
14	POLR2A	chr2:233940223-233941200	GM18951	blood:	n/a	n/a
15	MYC	chr2:233939768-233941082	NB4	blood:	n/a	chr2:233940271-233940281
16	POLR2A	chr2:233939509-233941199	GM18505	blood:	n/a	n/a
17	POLR2A	chr2:233939479-233941216	GM12892	blood:	n/a	n/a
18	POLR2A	chr2:233939998-233940288	K562	blood:	n/a	n/a
19	POLR2A	chr2:233940151-233940582	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:233939555-233941240	GM12891	blood:	n/a	n/a
21	POLR2A	chr2:233939777-233941193	GM12892	blood:	n/a	n/a
22	POLR2A	chr2:233939424-233941275	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:233939431-233941918	GM12878	blood:	n/a	n/a
24	RUNX3	chr2:233940256-233941121	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:233939755-233941248	GM19099	blood:	n/a	n/a
26	POLR2A	chr2:233939469-233941228	GM12892	blood:	n/a	n/a
27	POLR2A	chr2:233939574-233941295	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:233939676-233941263	GM12892	blood:	n/a	n/a
29	MTA3	chr2:233939413-233941203	GM12878	blood:	n/a	n/a
30	MAX	chr2:233939601-233941073	NB4	blood:	n/a	chr2:233940271-233940281
31	FOXA2	chr2:233939918-233940364	HepG2	liver:	n/a	n/a
32	POLR2A	chr2:233939658-233941202	GM19193	blood:	n/a	n/a
33	POLR2A	chr2:233940203-233941212	Raji	blood:	n/a	n/a
34	STAT5A	chr2:233940172-233941220	GM12878	blood:	n/a	n/a
35	POU2F2	chr2:233940275-233941124	GM12891	blood:	n/a	chr2:233940901-233940911 chr2:233940899-233940914 chr2:233940903-233940910 chr2:233940901-233940911 chr2:233940903-233940911 chr2:233940900-233940913 chr2:233940900-233940912 chr2:233940902-233940913 chr2:233940902-233940911 chr2:233940900-233940914 chr2:233940898-233940916 chr2:233940902-233940912
36	POLR2A	chr2:233939517-233941282	GM12892	blood:	n/a	n/a
37	POLR2A	chr2:233940214-233940365	HepG2	liver:	n/a	n/a
38	PML	chr2:233940143-233941260	GM12878	blood:	n/a	n/a
39	CHD2	chr2:233940146-233941204	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:233940067-233941155	GM15510	blood:	n/a	n/a
41	POLR2A	chr2:233939592-233941198	NB4	blood:	n/a	n/a

Variant related genes	Relation type
INPP5D	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11901943	1.00[EUR][1000 genomes]
rs28631381	1.00[AMR][1000 genomes]
rs57218566	1.00[EUR][1000 genomes]
rs58480585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61351720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61750834	1.00[AMR][1000 genomes]
rs6437087	1.00[EUR][1000 genomes]
rs6708294	1.00[EUR][1000 genomes]
rs6712466	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094946	1.00[EUR][1000 genomes]
rs73094949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094951	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094987	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73101521	1.00[EUR][1000 genomes]
rs73101525	1.00[EUR][1000 genomes]
rs73102744	1.00[AMR][1000 genomes]
rs73107107	1.00[AMR][1000 genomes]
rs73107126	1.00[EUR][1000 genomes]
rs73108362	1.00[AMR][1000 genomes]
rs9917365	1.00[EUR][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	nsv876009	chr2:233799400-233996429	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv876012	chr2:233899377-233996429	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233932600-233940400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:233937600-233943800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:233937600-233946400	Genic enhancers	Primary hematopoietic stem cells	blood
4	chr2:233938000-233940600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:233939000-233941000	Enhancers	Esophagus	oesophagus
6	chr2:233939000-233941800	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr2:233939200-233940600	Enhancers	Colonic Mucosa	Colon
8	chr2:233939200-233941000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:233939200-233943000	Enhancers	Fetal Thymus	thymus
10	chr2:233939400-233940600	Enhancers	Placenta	Placenta
11	chr2:233939400-233942600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:233939600-233940400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
13	chr2:233939600-233940400	Enhancers	HepG2	liver
14	chr2:233939600-233941000	Enhancers	Psoas Muscle	Psoas
15	chr2:233939600-233941200	Enhancers	Small Intestine	intestine
16	chr2:233939600-233941600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr2:233939600-233941800	Enhancers	Adipose Nuclei	Adipose
18	chr2:233939600-233941800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:233939600-233942000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr2:233939800-233940400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
21	chr2:233939800-233940400	Enhancers	Thymus	Thymus
22	chr2:233939800-233940600	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr2:233939800-233941200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:233939800-233941200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:233939800-233941200	Enhancers	Fetal Muscle Leg	muscle
26	chr2:233939800-233941200	Enhancers	Left Ventricle	heart
27	chr2:233939800-233941200	Enhancers	Stomach Mucosa	stomach
28	chr2:233939800-233941400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:233939800-233941600	Enhancers	Brain Anterior Caudate	brain
30	chr2:233939800-233941800	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr2:233939800-233941800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:233940000-233940800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:233940000-233941000	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr2:233940000-233941000	Enhancers	Right Atrium	heart
35	chr2:233940000-233941200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr2:233940000-233941200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr2:233940000-233941200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:233940000-233941200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr2:233940000-233941200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr2:233940000-233941200	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr2:233940000-233941200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr2:233940000-233941200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr2:233940000-233941200	Enhancers	Brain Cingulate Gyrus	brain
44	chr2:233940000-233941200	Enhancers	Fetal Brain Male	brain
45	chr2:233940000-233941200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:233940000-233941800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr2:233940000-233941800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr2:233940000-233941800	Enhancers	Brain Hippocampus Middle	brain
49	chr2:233940000-233942000	Enhancers	HUVEC	blood vessel
50	chr2:233940200-233940400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links