Variant report

Variant	rs13128841
Chromosome Location	chr4:102088150-102088151
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102086824..102091694-chr4:102266945..102270646,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138814	Chromatin interaction
ENSG00000254531	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10005338	0.86[EUR][1000 genomes]
rs10018021	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10025780	0.86[EUR][1000 genomes]
rs10030389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10050301	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10516471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13103902	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111186	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13112866	0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs13118966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13125501	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13135924	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13142024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1810024	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880943	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2048072	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2063058	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2174680	0.84[EUR][1000 genomes]
rs2659552	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2695215	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2695217	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2695219	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804361	0.86[EUR][1000 genomes]
rs3804368	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs3811063	0.88[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs3827770	0.81[EUR][1000 genomes]
rs4590038	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4698912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4698913	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4699106	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4699116	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs4699127	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs7677550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs950177	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9884638	0.85[EUR][1000 genomes]
rs9995338	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2760883	chr4:102081357-102088150	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102062600-102090400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:102078400-102093200	Weak transcription	HUVEC	blood vessel
3	chr4:102078400-102096600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:102078600-102088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:102078600-102090200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:102078800-102096000	Weak transcription	Ovary	ovary
7	chr4:102079000-102088800	Weak transcription	Fetal Intestine Small	intestine
8	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr4:102079600-102088800	Weak transcription	Psoas Muscle	Psoas
10	chr4:102079800-102096400	Weak transcription	Adipose Nuclei	Adipose
11	chr4:102080000-102092200	Weak transcription	NHDF-Ad	bronchial
12	chr4:102080000-102092600	Weak transcription	NH-A	brain
13	chr4:102080400-102088800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:102080600-102093000	Weak transcription	NHLF	lung
15	chr4:102080600-102100600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:102081000-102090200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:102082600-102090000	Weak transcription	Primary B cells from cord blood	blood
18	chr4:102083000-102088400	Weak transcription	Brain Anterior Caudate	brain
19	chr4:102083000-102096200	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:102083200-102096800	Weak transcription	Brain Angular Gyrus	brain
21	chr4:102084000-102089200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:102084200-102088800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:102084200-102103400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:102084600-102089400	Weak transcription	Brain Substantia Nigra	brain
25	chr4:102084800-102090200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:102084800-102092000	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:102085400-102090400	Weak transcription	Esophagus	oesophagus
28	chr4:102085400-102094200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:102085600-102096600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:102086000-102088200	Weak transcription	Small Intestine	intestine
31	chr4:102086800-102089800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr4:102087200-102090600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:102087200-102090600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:102087400-102088400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:102087400-102090600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:102087600-102090200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr4:102087600-102090200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:102087600-102093200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:102087600-102096400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:102087800-102088800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:102087800-102089800	Weak transcription	Liver	Liver
42	chr4:102087800-102092400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:102088000-102088200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr4:102088000-102089800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:102088000-102089800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:102088000-102089800	Enhancers	HMEC	breast
47	chr4:102088000-102089800	Enhancers	NHEK	skin
48	chr4:102088000-102094400	Enhancers	A549	lung

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