Variant report

Variant	rs949681
Chromosome Location	chr4:106131025-106131026
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	chr4:106067752..106071127-chr4:106128576..106132831,4	MCF-7	breast:
2	chr4:106127404..106129438-chr4:106130383..106133237,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1114718	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11933960	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12498609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12506006	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12511800	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12640842	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12642165	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12647779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12647884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1391442	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17583579	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17583593	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17616993	0.84[EUR][1000 genomes]
rs2023841	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2088484	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636697	1.00[MEX][hapmap]
rs2866774	0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34485921	0.83[AFR][1000 genomes]
rs6533180	0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533185	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs6533186	1.00[CEU][hapmap]
rs9637601	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106101000-106146600	Weak transcription	Spleen	Spleen
2	chr4:106106000-106135000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:106106200-106155000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr4:106113000-106154800	Weak transcription	Fetal Thymus	thymus
5	chr4:106113200-106136000	Weak transcription	Brain Anterior Caudate	brain
6	chr4:106113200-106136000	Weak transcription	Brain Substantia Nigra	brain
7	chr4:106113200-106136800	Weak transcription	Fetal Kidney	kidney
8	chr4:106113200-106146600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:106113600-106136000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:106113600-106173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:106113600-106195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:106114400-106136200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:106114400-106155200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:106114600-106134400	Weak transcription	Liver	Liver
15	chr4:106114600-106136000	Weak transcription	Pancreas	Pancrea
16	chr4:106114600-106145400	Weak transcription	Adipose Nuclei	Adipose
17	chr4:106114600-106155600	Weak transcription	Esophagus	oesophagus
18	chr4:106116400-106131600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:106117600-106136000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:106118000-106136200	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:106118000-106136800	Weak transcription	HSMMtube	muscle
22	chr4:106118000-106155400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:106118200-106135600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:106118400-106135800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:106118800-106131400	Weak transcription	Fetal Intestine Small	intestine
26	chr4:106118800-106131400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:106118800-106131600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:106118800-106135000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:106118800-106136000	Weak transcription	NH-A	brain
30	chr4:106118800-106136800	Weak transcription	Fetal Intestine Large	intestine
31	chr4:106118800-106136800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:106118800-106137000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:106118800-106155000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:106118800-106155200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:106119000-106135800	Weak transcription	HSMM	muscle
36	chr4:106119400-106131600	Weak transcription	NHEK	skin
37	chr4:106120000-106135600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:106120000-106135800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:106120000-106136400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:106122200-106137200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr4:106124000-106131800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:106124200-106136600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr4:106124400-106136400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:106124400-106137000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:106124800-106136400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:106126200-106132200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:106127000-106133800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr4:106127400-106131200	Strong transcription	Primary B cells from cord blood	blood
49	chr4:106127600-106136000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:106127600-106146600	Weak transcription	Left Ventricle	heart

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