Variant report

Variant	rs41344750
Chromosome Location	chr4:57830213-57830214
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	chr1:149223629..149225361-chr4:57830063..57832161,2	MCF-7	breast:
2	chr4:57830075..57832826-chr4:57843564..57845499,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000084092	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10002090	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10023009	0.89[AMR][1000 genomes]
rs10026915	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10034395	0.89[AMR][1000 genomes]
rs11573061	0.82[CEU][hapmap]
rs11573112	0.87[YRI][hapmap]
rs11573113	1.00[YRI][hapmap]
rs11935933	0.88[EUR][1000 genomes]
rs11942607	0.80[EUR][1000 genomes]
rs1277296	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs13146782	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17182939	0.82[CEU][hapmap]
rs17828496	1.00[EUR][1000 genomes]
rs1961950	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2227902	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2227903	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2271806	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs2271807	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs2276896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28370990	0.89[AMR][1000 genomes]
rs28474684	0.89[AMR][1000 genomes]
rs28520821	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28545156	0.89[AMR][1000 genomes]
rs28623722	0.89[AMR][1000 genomes]
rs28681160	0.89[AMR][1000 genomes]
rs28719609	0.89[AMR][1000 genomes]
rs3755901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs3755904	1.00[YRI][hapmap]
rs3775083	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs55734441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56798906	0.89[AMR][1000 genomes]
rs6554404	0.82[CEU][hapmap]
rs6837593	0.82[CEU][hapmap];0.80[CHB][hapmap]
rs6843415	0.89[AMR][1000 genomes]
rs73242618	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73242619	0.97[EUR][1000 genomes]
rs73242620	1.00[EUR][1000 genomes]
rs73242621	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73242622	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73242623	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73242625	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73242632	0.89[AMR][1000 genomes]
rs7654665	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs7673980	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57793600-57842000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:57793600-57842000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:57805000-57830800	Weak transcription	Colonic Mucosa	Colon
4	chr4:57820200-57836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:57820200-57836000	Weak transcription	Esophagus	oesophagus
6	chr4:57821600-57832600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:57822600-57832600	Weak transcription	Fetal Brain Male	brain
8	chr4:57824000-57831400	Weak transcription	Right Ventricle	heart
9	chr4:57824400-57830400	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:57824600-57838400	Weak transcription	Aorta	Aorta
11	chr4:57825200-57830600	Weak transcription	Brain Substantia Nigra	brain
12	chr4:57825200-57830800	Weak transcription	HUVEC	blood vessel
13	chr4:57825200-57832400	Weak transcription	A549	lung
14	chr4:57825400-57830600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:57825400-57830600	Weak transcription	K562	blood
16	chr4:57825400-57830800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:57825400-57831000	Weak transcription	Fetal Kidney	kidney
18	chr4:57825600-57830400	Weak transcription	NHLF	lung
19	chr4:57825600-57832200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:57825600-57832600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:57825600-57838600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:57826000-57830600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:57826000-57832000	Weak transcription	Psoas Muscle	Psoas
24	chr4:57826400-57831800	Weak transcription	Gastric	stomach
25	chr4:57826400-57839800	Strong transcription	Primary T cells from cord blood	blood
26	chr4:57826600-57832200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:57826600-57833400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:57826600-57834400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr4:57826600-57834600	Strong transcription	Fetal Stomach	stomach
30	chr4:57826600-57835200	Strong transcription	Brain Anterior Caudate	brain
31	chr4:57826600-57838600	Strong transcription	Fetal Intestine Small	intestine
32	chr4:57826600-57838800	Strong transcription	Liver	Liver
33	chr4:57826600-57839000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:57826600-57839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:57826600-57840800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:57826600-57840800	Strong transcription	Fetal Brain Female	brain
37	chr4:57826600-57840800	Strong transcription	Fetal Muscle Leg	muscle
38	chr4:57826600-57840800	Strong transcription	Fetal Thymus	thymus
39	chr4:57826600-57841000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:57826600-57841400	Strong transcription	Fetal Intestine Large	intestine
41	chr4:57826800-57839000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:57826800-57840800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:57826800-57840800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:57826800-57840800	Weak transcription	Stomach Mucosa	stomach
45	chr4:57827000-57832800	Strong transcription	Brain Cingulate Gyrus	brain
46	chr4:57827000-57838400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:57827000-57840400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:57827000-57843200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr4:57827200-57832600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:57827200-57833600	Strong transcription	Thymus	Thymus

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