Variant report

Variant	rs9682043
Chromosome Location	chr3:150137276-150137277
allele	A/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	FOS	chr3:150136925-150137632	MCF10A-Er-Src	breast:	n/a	chr3:150137487-150137494 chr3:150137555-150137567 chr3:150137486-150137494
2	FOS	chr3:150136884-150137565	MCF10A-Er-Src	breast:	n/a	chr3:150137487-150137494 chr3:150137486-150137494
3	POLR2A	chr3:150137221-150137655	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:150135087-150138468	K562	blood:	n/a	n/a
5	FOSL1	chr3:150136889-150137327	HCT-116	colon:	n/a	n/a
6	STAT3	chr3:150137103-150137448	MCF10A-Er-Src	breast:	n/a	n/a
7	JUN	chr3:150136968-150137369	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:149955070..149958943-chr3:150133193..150137279,5	MCF-7	breast:
2	chr3:150134729..150137378-chr3:150149401..150152677,3	MCF-7	breast:
3	chr3:150130662..150134020-chr3:150134493..150137721,4	MCF-7	breast:
4	chr3:150088147..150089862-chr3:150135989..150138013,2	MCF-7	breast:

Variant related genes	Relation type
TSC22D2	TF binding region
ENSG00000244541	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11706784	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12054166	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs13069723	0.92[ASN][1000 genomes]
rs13092207	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13092341	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13097358	0.91[MEX][hapmap]
rs16862623	0.84[CEU][hapmap]
rs16862648	0.89[CHD][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs2068659	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28517277	0.85[ASN][1000 genomes]
rs33988810	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34192407	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34384576	0.85[ASN][1000 genomes]
rs34518530	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34616287	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34991086	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35500085	0.86[EUR][1000 genomes]
rs35704634	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35725711	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35982655	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56040746	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62269065	0.92[ASN][1000 genomes]
rs6440677	0.82[MEX][hapmap]
rs6763024	0.88[ASN][1000 genomes]
rs879634	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1799287	chr3:150125721-150147118	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9682043	RAP2B	cis	cerebellum	SCAN
rs9682043	TSC22D2	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150125000-150137400	Active TSS	GM12878-XiMat	blood
2	chr3:150131000-150138600	Weak transcription	Lung	lung
3	chr3:150131000-150152000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:150131000-150166000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:150131200-150138600	Enhancers	Colon Smooth Muscle	Colon
6	chr3:150131400-150138600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:150132200-150140600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:150132400-150139200	Weak transcription	Fetal Stomach	stomach
9	chr3:150132400-150146000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:150132400-150151400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:150132400-150151600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:150132400-150159200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:150132400-150160400	Weak transcription	Pancreas	Pancrea
14	chr3:150132400-150175000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:150132400-150175000	Weak transcription	Placenta	Placenta
16	chr3:150132600-150137800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:150132600-150145200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:150132800-150138200	Enhancers	Brain Substantia Nigra	brain
19	chr3:150132800-150145800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:150132800-150145800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:150132800-150151000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:150133000-150139800	Weak transcription	Fetal Kidney	kidney
23	chr3:150133400-150137400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:150133400-150137600	Genic enhancers	HSMM	muscle
25	chr3:150133600-150139600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:150133600-150139800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:150133600-150151000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:150133600-150159200	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:150133600-150159200	Weak transcription	Left Ventricle	heart
30	chr3:150133800-150159200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:150134000-150137400	Weak transcription	Right Atrium	heart
32	chr3:150134000-150138600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:150134000-150143000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:150134000-150143800	Weak transcription	Aorta	Aorta
35	chr3:150134000-150146000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:150134000-150147000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:150134000-150159200	Weak transcription	Thymus	Thymus
38	chr3:150134200-150139200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:150134200-150140800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:150134400-150137600	Enhancers	Primary T cells from cord blood	blood
41	chr3:150134400-150138600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:150134400-150139200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:150134600-150146000	Weak transcription	Stomach Mucosa	stomach
44	chr3:150134600-150174800	Weak transcription	Dnd41	blood
45	chr3:150134800-150139800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:150135000-150137400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:150135000-150139200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:150135000-150175600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:150135200-150138000	Enhancers	Small Intestine	intestine
50	chr3:150135200-150138200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links