Variant report

Variant	rs41393845
Chromosome Location	chr2:171677752-171677753
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	CTBP2	chr2:171676326-171681103	H1-hESC	embryonic stem cell:	n/a	n/a
2	PML	chr2:171677418-171677774	K562	blood:	n/a	n/a
3	EP300	chr2:171677453-171677775	K562	blood:	n/a	n/a
4	POLR2A	chr2:171677325-171677784	H1-neurons	neurons:	n/a	n/a
5	CEBPD	chr2:171677356-171677830	K562	blood:	n/a	n/a
6	GABPA	chr2:171677465-171677766	K562	blood:	n/a	n/a
7	GATA2	chr2:171677339-171677756	K562	blood:	n/a	n/a
8	JUND	chr2:171677664-171677892	H1-hESC	embryonic stem cell:	n/a	chr2:171677862-171677873 chr2:171677861-171677869
9	POLR2A	chr2:171677368-171677830	K562	blood:	n/a	n/a
10	TEAD4	chr2:171677305-171677844	K562	blood:	n/a	n/a
11	NR2F2	chr2:171677347-171677765	K562	blood:	n/a	n/a
12	POLR2A	chr2:171677005-171680495	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr2:171677464-171677781	K562	blood:	n/a	n/a
14	TAL1	chr2:171677403-171677820	K562	blood:	n/a	n/a
15	CCNT2	chr2:171677455-171677768	K562	blood:	n/a	n/a
16	SUZ12	chr2:171676388-171680031	H1-hESC	embryonic stem cell:	n/a	n/a
17	CBX3	chr2:171677407-171677754	K562	blood:	n/a	n/a
18	GATA1	chr2:171677081-171680037	PBDE	blood:	n/a	chr2:171679713-171679722 chr2:171679319-171679327 chr2:171678862-171678872 chr2:171679660-171679673
19	SIN3A	chr2:171677455-171678029	H1-hESC	embryonic stem cell:	n/a	n/a
20	TEAD4	chr2:171677308-171677787	K562	blood:	n/a	n/a
21	NR2F2	chr2:171677292-171677857	K562	blood:	n/a	n/a
22	STAT5A	chr2:171677299-171677813	K562	blood:	n/a	chr2:171677468-171677479

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171675485..171677773-chr2:171677982..171679731,3	K562	blood:
2	chr2:171673426..171677773-chr2:171677821..171680534,5	K562	blood:

Variant related genes	Relation type
ENSG00000235934	TF binding region
GAD1	TF binding region
ENSG00000128683	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs16823157	0.89[AMR][1000 genomes]
rs17694726	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17700577	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17700773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751683	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1894918	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2160414	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3791875	0.80[AMR][1000 genomes]
rs3791879	0.80[AMR][1000 genomes]
rs45465192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45467694	0.81[AMR][1000 genomes]
rs45471500	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs45473292	1.00[AMR][1000 genomes]
rs45486908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45506192	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs45626540	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4667653	0.92[AMR][1000 genomes]
rs4667654	0.92[AMR][1000 genomes]
rs4667655	0.89[AMR][1000 genomes]
rs4667659	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4667660	0.86[AMR][1000 genomes]
rs4667661	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4668307	0.89[AMR][1000 genomes]
rs4668310	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668311	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668318	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668319	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4668330	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56852746	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs701491	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs769406	0.81[AMR][1000 genomes];0.87[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	esv1806894	chr2:171651783-171679041	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv528929	chr2:171672191-171678379	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171674400-171677800	Bivalent Enhancer	Fetal Intestine Large	intestine
2	chr2:171674400-171682200	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:171675600-171678000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:171675600-171678200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:171676200-171679400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
6	chr2:171676400-171677800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:171676400-171679000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
8	chr2:171676400-171679000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
9	chr2:171676400-171679200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr2:171676400-171679400	Bivalent Enhancer	Fetal Thymus	thymus
11	chr2:171676400-171679600	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr2:171676400-171679800	Bivalent Enhancer	Fetal Stomach	stomach
13	chr2:171676600-171677800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:171676600-171678000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:171676600-171679400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
16	chr2:171676600-171679400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
17	chr2:171676800-171677800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
18	chr2:171676800-171677800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr2:171676800-171677800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
20	chr2:171676800-171677800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
21	chr2:171676800-171677800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
22	chr2:171676800-171677800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
23	chr2:171676800-171678000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
24	chr2:171676800-171678000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:171676800-171678000	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
26	chr2:171676800-171678000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
27	chr2:171676800-171678000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
28	chr2:171676800-171678200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
29	chr2:171676800-171678400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:171676800-171678400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
31	chr2:171676800-171678800	Flanking Active TSS	Right Ventricle	heart
32	chr2:171676800-171679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:171676800-171679200	Bivalent Enhancer	Lung	lung
34	chr2:171676800-171679600	Enhancers	Gastric	stomach
35	chr2:171676800-171679800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr2:171676800-171680000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
37	chr2:171676800-171680600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:171676800-171680600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
39	chr2:171676800-171681200	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
40	chr2:171677000-171677800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:171677000-171677800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
42	chr2:171677000-171677800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:171677000-171677800	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
44	chr2:171677000-171677800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
45	chr2:171677000-171677800	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
46	chr2:171677000-171677800	Bivalent Enhancer	Small Intestine	intestine
47	chr2:171677000-171677800	Flanking Bivalent TSS/Enh	HMEC	breast
48	chr2:171677000-171678000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:171677000-171678000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:171677000-171678000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood

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