Variant report

Variant	rs4663136
Chromosome Location	chr2:234197717-234197718
allele	C/G
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	CEBPB	chr2:234197670-234197757	K562	blood:	n/a	chr2:234197712-234197723
2	GATA3	chr2:234197369-234197735	MCF-7	breast:	n/a	n/a
3	HDAC2	chr2:234197241-234197755	MCF-7	breast:	n/a	n/a
4	GATA2	chr2:234197347-234197721	SH-SY5Y	brain:	n/a	n/a
5	ZNF217	chr2:234197320-234197794	MCF-7	breast:	n/a	n/a
6	TCF7L2	chr2:234197342-234197729	MCF-7	breast:	n/a	n/a
7	FOXA1	chr2:234197465-234197745	T-47D	breast:	n/a	n/a
8	SIN3AK20	chr2:234197187-234198005	MCF-7	breast:	n/a	n/a
9	CEBPB	chr2:234197702-234197756	HepG2	liver:	n/a	chr2:234197712-234197723
10	NR2F2	chr2:234197289-234197957	MCF-7	breast:	n/a	n/a
11	GATA3	chr2:234197304-234197723	T-47D	breast:	n/a	n/a
12	GATA3	chr2:234197315-234197804	MCF-7	breast:	n/a	n/a
13	GATA3	chr2:234197221-234197965	MCF-7	breast:	n/a	n/a
14	GATA3	chr2:234197457-234197740	SH-SY5Y	brain:	n/a	n/a
15	GATA3	chr2:234197332-234197945	MCF-7	breast:	n/a	n/a
16	HDAC2	chr2:234197289-234197779	MCF-7	breast:	n/a	n/a
17	CEBPB	chr2:234197477-234197927	MCF-7	breast:	n/a	chr2:234197712-234197723

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234159075..234160799-chr2:234195887..234199490,3	MCF-7	breast:

Variant related genes	Relation type
ATG16L1	TF binding region
ENSG00000085978	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1045095	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10929033	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11685932	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs11894529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13005285	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs1596016	0.81[ASN][1000 genomes]
rs1816753	0.85[ASN][1000 genomes]
rs2119504	0.85[ASN][1000 genomes]
rs2241876	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241877	0.94[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2289475	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35812841	0.87[ASN][1000 genomes]
rs3749079	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792110	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4663429	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6431259	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6431262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6431655	0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs6431659	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs6737398	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs6754677	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs6861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7587633	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7595748	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4663136	ATG16L1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234162200-234205200	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:234162200-234205200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:234162400-234205200	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr2:234162400-234205400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:234162600-234205000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:234162600-234205200	Strong transcription	Fetal Muscle Leg	muscle
7	chr2:234162800-234205600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:234163200-234206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:234164200-234205400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:234164200-234205400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:234164600-234206000	Strong transcription	HepG2	liver
12	chr2:234165000-234206000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:234165200-234205400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:234166800-234206000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:234172200-234204800	Strong transcription	Placenta	Placenta
16	chr2:234176800-234207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:234177000-234206000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:234177200-234205400	Strong transcription	Dnd41	blood
19	chr2:234178400-234205200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:234179000-234206200	Strong transcription	Fetal Thymus	thymus
21	chr2:234179200-234205600	Strong transcription	Fetal Brain Female	brain
22	chr2:234179600-234204000	Strong transcription	HUVEC	blood vessel
23	chr2:234179600-234205400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:234179600-234205400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:234179600-234205600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:234179800-234205200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr2:234180800-234206400	Strong transcription	Thymus	Thymus
28	chr2:234181000-234205200	Strong transcription	Liver	Liver
29	chr2:234181400-234216400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:234182400-234206000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:234183000-234204400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:234186800-234198200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:234187200-234198200	Weak transcription	Fetal Heart	heart
34	chr2:234187400-234198000	Weak transcription	Fetal Kidney	kidney
35	chr2:234189200-234205200	Strong transcription	Brain Germinal Matrix	brain
36	chr2:234189200-234205400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:234189200-234205600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:234189600-234205200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr2:234189800-234204600	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr2:234189800-234205200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:234190000-234205000	Strong transcription	Aorta	Aorta
42	chr2:234190000-234205600	Strong transcription	Fetal Intestine Small	intestine
43	chr2:234190200-234205400	Strong transcription	Spleen	Spleen
44	chr2:234190600-234205600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:234190600-234206600	Strong transcription	Fetal Stomach	stomach
46	chr2:234191600-234198800	Weak transcription	Fetal Brain Male	brain
47	chr2:234192000-234206000	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:234192400-234205000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:234192600-234197800	Weak transcription	Small Intestine	intestine
50	chr2:234193000-234205000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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