Variant report

Variant	rs4241549
Chromosome Location	chr3:88122989-88122990
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88106550..88112808-chr3:88121640..88129198,13	MCF-7	breast:
2	chr3:88120312..88123363-chr3:88127498..88130221,3	K562	blood:
3	chr3:88111449..88113994-chr3:88120532..88124879,4	K562	blood:

Variant related genes	Relation type
ENSG00000229729	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11128023	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1367615	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431154	1.00[EUR][1000 genomes]
rs1594453	1.00[EUR][1000 genomes]
rs1594455	1.00[EUR][1000 genomes]
rs1604700	1.00[EUR][1000 genomes]
rs1897238	1.00[EUR][1000 genomes]
rs2033390	1.00[EUR][1000 genomes]
rs2567037	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735557	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241550	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287925	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4404474	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4425287	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443201	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4513473	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4515075	1.00[EUR][1000 genomes]
rs4616669	1.00[EUR][1000 genomes]
rs4858927	1.00[EUR][1000 genomes]
rs4858933	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858970	1.00[EUR][1000 genomes]
rs4858987	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4858988	0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4858989	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551270	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7615309	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621357	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7625641	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633215	0.88[ASN][1000 genomes]
rs7633486	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636845	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7650749	1.00[EUR][1000 genomes]
rs7650912	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650915	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs930154	1.00[EUR][1000 genomes]
rs9310062	1.00[EUR][1000 genomes]
rs9310063	1.00[EUR][1000 genomes]
rs9310064	0.86[AFR][1000 genomes]
rs9310069	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310073	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812903	1.00[EUR][1000 genomes]
rs9833231	1.00[EUR][1000 genomes]
rs9850550	1.00[EUR][1000 genomes]
rs9860113	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9864564	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867614	1.00[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	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88109400-88124400	Weak transcription	Pancreas	Pancrea
2	chr3:88110200-88124200	Weak transcription	Fetal Kidney	kidney
3	chr3:88111400-88124200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:88111400-88133600	Weak transcription	Brain Angular Gyrus	brain
5	chr3:88111400-88136200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:88111400-88136200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:88111600-88123200	Weak transcription	Liver	Liver
8	chr3:88111600-88124000	Weak transcription	Right Atrium	heart
9	chr3:88111600-88124000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:88111600-88124000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:88111600-88124200	Weak transcription	Fetal Lung	lung
12	chr3:88111600-88135200	Weak transcription	HSMM	muscle
13	chr3:88111600-88135400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:88111600-88135600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:88111800-88123600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:88111800-88135400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:88112200-88136600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:88112200-88154200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:88112400-88124400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:88112400-88143600	Weak transcription	HUVEC	blood vessel
21	chr3:88113200-88146200	Weak transcription	HMEC	breast
22	chr3:88113800-88123000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:88113800-88134800	Weak transcription	Dnd41	blood
24	chr3:88115200-88133400	Weak transcription	Left Ventricle	heart
25	chr3:88115600-88124000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:88116800-88124200	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:88116800-88139800	Weak transcription	Thymus	Thymus
28	chr3:88117000-88124400	Weak transcription	Right Ventricle	heart
29	chr3:88117000-88133800	Weak transcription	Aorta	Aorta
30	chr3:88117000-88135800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:88117400-88124600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:88117600-88123800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:88118000-88124200	Weak transcription	Fetal Heart	heart
34	chr3:88118000-88128800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:88118200-88124000	Weak transcription	K562	blood
36	chr3:88118800-88124200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:88119600-88123600	Weak transcription	Small Intestine	intestine
38	chr3:88120600-88128600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:88120600-88135400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:88121000-88135400	Weak transcription	Fetal Thymus	thymus
41	chr3:88121400-88136400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:88121600-88129000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:88121600-88130200	Weak transcription	Primary B cells from cord blood	blood
44	chr3:88121800-88123600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:88121800-88123800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:88121800-88130800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:88121800-88141800	Weak transcription	NHLF	lung
48	chr3:88122200-88124800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr3:88122400-88123200	Enhancers	Primary T cells from cord blood	blood
50	chr3:88122400-88123200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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