Variant report

Variant	rs2241542
Chromosome Location	chr3:42591943-42591944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42586339..42588894-chr3:42591733..42594532,2	MCF-7	breast:
2	chr3:42590321..42592623-chr3:42611370..42613403,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1062051	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13089845	0.83[ASN][1000 genomes]
rs13090902	0.83[ASN][1000 genomes]
rs13093680	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13095447	0.80[ASN][1000 genomes]
rs17074602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074662	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17074664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17074669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17074674	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17074680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2271182	0.82[ASN][1000 genomes]
rs2284303	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2300057	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2302352	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs339713	1.00[CEU][hapmap]
rs33984028	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs34801786	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs34852409	0.81[ASN][1000 genomes]
rs35676838	0.83[ASN][1000 genomes]
rs35770315	0.88[EUR][1000 genomes]
rs3774401	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774407	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs3821836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3846059	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs3846061	1.00[CEU][hapmap]
rs3886782	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3901239	1.00[CEU][hapmap]
rs6441928	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs66786953	0.81[ASN][1000 genomes]
rs6772312	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6788548	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6792277	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7617403	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7617736	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7624628	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs890688	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][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	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42575200-42594400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:42577400-42592800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:42577600-42592000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:42578400-42593200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:42578400-42593400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:42581800-42594400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:42582000-42593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:42582000-42593600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:42582000-42594400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:42582200-42594400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:42582800-42592000	Weak transcription	Ovary	ovary
13	chr3:42586000-42593400	Weak transcription	NH-A	brain
14	chr3:42586200-42595000	Weak transcription	Fetal Brain Male	brain
15	chr3:42586400-42593200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:42586400-42593800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:42586400-42594400	Weak transcription	NHEK	skin
18	chr3:42586600-42593400	Weak transcription	A549	lung
19	chr3:42586600-42593800	Weak transcription	Right Ventricle	heart
20	chr3:42587000-42594200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:42587000-42594200	Weak transcription	HSMMtube	muscle
22	chr3:42587000-42594400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:42587000-42602400	Weak transcription	Colonic Mucosa	Colon
24	chr3:42587400-42597000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:42587400-42597200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:42587400-42606800	Weak transcription	Small Intestine	intestine
27	chr3:42587600-42594400	Weak transcription	HepG2	liver
28	chr3:42587800-42597000	Strong transcription	Fetal Thymus	thymus
29	chr3:42587800-42597000	Strong transcription	Thymus	Thymus
30	chr3:42587800-42611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:42588000-42613000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:42588400-42593400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:42588400-42613000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:42588600-42618000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:42589000-42593800	Weak transcription	K562	blood
36	chr3:42589000-42594200	Weak transcription	NHDF-Ad	bronchial
37	chr3:42589000-42594600	Weak transcription	HSMM	muscle
38	chr3:42589000-42611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:42589200-42611000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:42589400-42592800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:42589400-42592800	Weak transcription	Placenta	Placenta
42	chr3:42589400-42593400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:42589400-42593400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:42589400-42593800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:42589400-42593800	Weak transcription	Psoas Muscle	Psoas
46	chr3:42589400-42594200	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:42589400-42594400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:42589400-42595400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:42589400-42596800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:42589400-42610800	Weak transcription	Stomach Mucosa	stomach

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