Variant report

Variant	rs1221002
Chromosome Location	chr3:150911683-150911684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150909405..150911951-chr3:150919073..150920609,2	MCF-7	breast:
2	chr3:150910511..150913182-chr3:150926797..150928825,2	K562	blood:
3	chr3:150911256..150912948-chr3:150913991..150916075,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1017348	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs10513387	0.89[CEU][hapmap]
rs1221003	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1221004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1231519	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1231520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13322794	0.83[CEU][hapmap]
rs1549829	0.89[CEU][hapmap]
rs1554120	0.89[CEU][hapmap]
rs17290219	0.89[CEU][hapmap]
rs1920397	1.00[CEU][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2141630	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2567325	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2700470	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4680158	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6440722	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792089	0.82[CEU][hapmap]
rs9818251	0.84[CEU][hapmap]
rs9836053	1.00[ASW][hapmap];0.89[CEU][hapmap]
rs9854126	0.84[CEU][hapmap]
rs9871624	0.89[CEU][hapmap]
rs9876268	0.82[CEU][hapmap]
rs9881116	0.84[CEU][hapmap]

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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1221002	MME	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150873800-150913800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
3	chr3:150889200-150914800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:150889600-150913800	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:150890600-150923400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:150896200-150927800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:150896600-150918200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:150897200-150916200	Weak transcription	Fetal Intestine Small	intestine
9	chr3:150897600-150913800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:150898600-150917200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:150899000-150917000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:150900400-150917200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:150900600-150917000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:150900800-150917200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:150901200-150917600	Weak transcription	Fetal Thymus	thymus
16	chr3:150901200-150917800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:150901400-150914200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:150901400-150916200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:150901600-150913600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:150901800-150918000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:150902200-150916400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:150904200-150911800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:150904600-150914000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:150904600-150914000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:150904600-150915200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:150904800-150911800	Weak transcription	Brain Anterior Caudate	brain
27	chr3:150904800-150916200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:150906000-150912400	Strong transcription	Primary hematopoietic stem cells	blood
29	chr3:150907000-150917400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:150907200-150916200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:150907400-150915800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:150907400-150916800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:150907800-150913200	Weak transcription	HepG2	liver
34	chr3:150908800-150913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:150908800-150933200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:150909000-150917200	Weak transcription	Dnd41	blood
37	chr3:150909000-150918800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:150909400-150913400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:150909600-150916200	Weak transcription	Fetal Intestine Large	intestine
40	chr3:150910000-150914600	Weak transcription	Primary T cells from cord blood	blood
41	chr3:150911400-150912400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:150911600-150918600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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