Variant report

Variant	rs12640842
Chromosome Location	chr4:106193588-106193589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106184567..106187118-chr4:106192794..106195271,2	MCF-7	breast:
2	chr4:106063671..106068178-chr4:106191918..106194890,4	MCF-7	breast:
3	chr4:106189275..106190947-chr4:106192972..106194915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1114718	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11933960	0.95[ASN][1000 genomes]
rs12498609	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506006	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12511800	0.94[ASN][1000 genomes]
rs12642165	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12647779	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12647884	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1391442	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17583579	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17583593	0.83[EUR][1000 genomes]
rs2023841	0.89[ASN][1000 genomes]
rs2088484	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2866774	0.94[ASN][1000 genomes]
rs6533180	0.95[ASN][1000 genomes]
rs6533185	1.00[CEU][hapmap]
rs6533186	1.00[CEU][hapmap]
rs949681	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9637601	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106113600-106195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:106154000-106198800	Weak transcription	Hela-S3	cervix
3	chr4:106156800-106196200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr4:106157400-106193600	Weak transcription	Colonic Mucosa	Colon
5	chr4:106163400-106196400	Weak transcription	Brain Angular Gyrus	brain
6	chr4:106178000-106201000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr4:106179200-106201000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:106180200-106199000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:106180400-106198800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:106181000-106196800	Weak transcription	A549	lung
11	chr4:106187200-106202000	Weak transcription	Stomach Mucosa	stomach
12	chr4:106188800-106199800	Strong transcription	GM12878-XiMat	blood
13	chr4:106189200-106197800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr4:106189400-106198400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:106189400-106198600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:106189600-106198000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:106189600-106198200	Strong transcription	Placenta	Placenta
18	chr4:106189600-106198400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:106189800-106194400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:106189800-106194800	Strong transcription	Fetal Intestine Large	intestine
21	chr4:106189800-106194800	Strong transcription	Fetal Muscle Leg	muscle
22	chr4:106189800-106197600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:106190000-106194400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:106190000-106197800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:106190000-106198600	Strong transcription	Fetal Thymus	thymus
26	chr4:106190200-106194400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:106190200-106197800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:106190200-106197800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:106190200-106197800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:106190200-106197800	Strong transcription	Fetal Lung	lung
31	chr4:106190200-106198000	Strong transcription	Liver	Liver
32	chr4:106190200-106198800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:106190400-106193600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:106190400-106194400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:106190400-106194400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr4:106190400-106194600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:106190400-106195600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:106190400-106197800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:106190400-106198000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:106190400-106198000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr4:106190400-106198000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:106190400-106198000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr4:106190400-106198400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:106190400-106198800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:106190400-106199000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:106190400-106199000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr4:106190600-106194000	Strong transcription	Osteobl	bone
48	chr4:106190600-106194200	Strong transcription	NH-A	brain
49	chr4:106190600-106194400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:106190600-106194400	Strong transcription	HSMMtube	muscle

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