Variant report

Variant	rs6578440
Chromosome Location	chr11:4098623-4098624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3861239..3864353-chr11:4095380..4099458,3	MCF-7	breast:
2	chr11:4098019..4101668-chr11:4102257..4105947,4	K562	blood:
3	chr11:4094295..4095900-chr11:4097505..4099335,2	K562	blood:

Variant related genes	Relation type
ENSG00000177105	Chromatin interaction
ENSG00000167323	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1042919	0.83[JPT][hapmap]
rs1042927	0.81[JPT][hapmap]
rs10742194	0.90[YRI][hapmap]
rs10742229	0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs10767827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767828	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767851	0.83[JPT][hapmap]
rs10767853	0.83[JPT][hapmap]
rs10835605	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030814	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs11030841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602757	0.82[YRI][hapmap]
rs1442725	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs1465952	0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs1561876	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1662162	0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1735068	0.83[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2289570	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs2898950	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs2923951	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs2959060	0.92[AFR][1000 genomes]
rs2959061	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs2959072	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs2959073	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs3794050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794051	0.90[AFR][1000 genomes]
rs3794052	0.92[AFR][1000 genomes]
rs4365044	0.89[CHB][hapmap]
rs4910595	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs4910874	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs4910881	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs4910882	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910895	0.83[JPT][hapmap]
rs4910896	0.81[JPT][hapmap]
rs4910897	0.81[JPT][hapmap]
rs4910908	0.81[JPT][hapmap]
rs4910909	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs4910910	0.83[JPT][hapmap]
rs4910911	0.83[JPT][hapmap]
rs4910912	0.83[JPT][hapmap]
rs6578446	0.81[JPT][hapmap]
rs6578448	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs7103860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7104462	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109811	0.84[AFR][1000 genomes]
rs7930739	0.94[AFR][1000 genomes]
rs7932271	0.82[JPT][hapmap]
rs7933164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7945532	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7945918	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs7946885	0.81[JPT][hapmap]
rs7951836	0.83[JPT][hapmap]
rs894455	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs9735835	0.90[AFR][1000 genomes]
rs992980	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4066200-4104200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:4066400-4107800	Weak transcription	Small Intestine	intestine
3	chr11:4070800-4108600	Weak transcription	HSMM	muscle
4	chr11:4076200-4103000	Weak transcription	Fetal Intestine Large	intestine
5	chr11:4079000-4112600	Weak transcription	Fetal Brain Female	brain
6	chr11:4081000-4101800	Weak transcription	Lung	lung
7	chr11:4081000-4104600	Weak transcription	Colonic Mucosa	Colon
8	chr11:4082600-4107400	Weak transcription	Stomach Mucosa	stomach
9	chr11:4082800-4103400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:4083200-4102200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:4086200-4102600	Weak transcription	Pancreas	Pancrea
12	chr11:4086200-4115200	Weak transcription	NHDF-Ad	bronchial
13	chr11:4087200-4102400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:4087600-4102400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:4087600-4115000	Weak transcription	HSMMtube	muscle
16	chr11:4087800-4107800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:4088000-4101800	Weak transcription	Aorta	Aorta
18	chr11:4088600-4107800	Weak transcription	Right Ventricle	heart
19	chr11:4090400-4102800	Weak transcription	Gastric	stomach
20	chr11:4091600-4102800	Weak transcription	Left Ventricle	heart
21	chr11:4091600-4107600	Weak transcription	Psoas Muscle	Psoas
22	chr11:4091800-4101600	Weak transcription	HepG2	liver
23	chr11:4093400-4102800	Weak transcription	Placenta	Placenta
24	chr11:4093600-4112600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:4093800-4102400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:4093800-4102600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:4093800-4103800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:4093800-4104000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:4093800-4115000	Weak transcription	Brain Germinal Matrix	brain
30	chr11:4093800-4115200	Weak transcription	Fetal Kidney	kidney
31	chr11:4094000-4100000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:4094000-4102200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr11:4094000-4102400	Weak transcription	Brain Anterior Caudate	brain
34	chr11:4094000-4103000	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:4094000-4103000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:4094000-4103800	Weak transcription	Fetal Lung	lung
37	chr11:4094000-4106200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr11:4094000-4107800	Weak transcription	Brain Angular Gyrus	brain
39	chr11:4094000-4108600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:4094000-4108600	Weak transcription	Osteobl	bone
41	chr11:4094000-4115000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:4094000-4115000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:4094000-4115200	Weak transcription	Brain Substantia Nigra	brain
44	chr11:4094400-4103200	Weak transcription	Colon Smooth Muscle	Colon
45	chr11:4094600-4102600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr11:4095800-4101600	Weak transcription	Adipose Nuclei	Adipose
47	chr11:4095800-4102600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:4095800-4109400	Weak transcription	K562	blood
49	chr11:4096000-4099400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:4096000-4099400	Weak transcription	Thymus	Thymus

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