Variant report

Variant	rs13139971
Chromosome Location	chr4:129801118-129801119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129731505..129733452-chr4:129799174..129801929,2	MCF-7	breast:
2	chr4:129798920..129801366-chr4:129805840..129808673,2	K562	blood:
3	chr4:129732016..129733966-chr4:129800387..129802773,2	K562	blood:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10518538	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10857133	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs11098988	0.94[ASN][1000 genomes]
rs11098989	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098991	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11722253	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs11722830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11730068	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11734137	0.80[ASN][1000 genomes]
rs11735343	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs11735359	0.88[EUR][1000 genomes]
rs11736731	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs11933240	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940298	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945441	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12505447	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs13110855	1.00[CHB][hapmap]
rs13110952	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13110956	0.82[ASN][1000 genomes]
rs13111413	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs13114904	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125643	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133798	0.88[EUR][1000 genomes]
rs13135764	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13136807	0.87[ASN][1000 genomes]
rs13143989	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs13146706	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13149221	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs17013734	1.00[CHB][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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 miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1026938	chr4:129770961-129936205	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv870175	chr4:129771718-129937945	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1026772	chr4:129773881-129936205	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv461637	chr4:129774375-129924977	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv595397	chr4:129774375-129924977	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv461638	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv595398	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1018994	chr4:129775612-129933968	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv4504	chr4:129777368-129803959	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv1034996	chr4:129777825-129905255	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv537249	chr4:129777825-129905255	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv1022446	chr4:129778025-129905116	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv537250	chr4:129778025-129905116	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv1030296	chr4:129778025-129920680	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
18	nsv537251	chr4:129778025-129920680	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
19	esv2830419	chr4:129785483-129905256	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
20	nsv533785	chr4:129785683-129857992	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a
21	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129779600-129809800	Weak transcription	Small Intestine	intestine
2	chr4:129789400-129811200	Weak transcription	Placenta	Placenta
3	chr4:129793200-129812200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:129793400-129801200	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:129793400-129804200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:129793600-129804200	Weak transcription	NHLF	lung
7	chr4:129793600-129812000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:129793600-129812200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:129793600-129812800	Weak transcription	Spleen	Spleen
10	chr4:129793600-129815400	Weak transcription	Fetal Lung	lung
11	chr4:129793600-129816800	Weak transcription	Lung	lung
12	chr4:129793600-129817200	Weak transcription	Psoas Muscle	Psoas
13	chr4:129793600-129825000	Weak transcription	Ovary	ovary
14	chr4:129793800-129801200	Weak transcription	Fetal Intestine Small	intestine
15	chr4:129793800-129811600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:129793800-129907200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:129794000-129806200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:129794000-129809200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:129794000-129813400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:129794000-129814800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:129794200-129803400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:129794200-129810800	Weak transcription	Fetal Brain Female	brain
23	chr4:129794200-129810800	Weak transcription	Right Ventricle	heart
24	chr4:129794200-129812000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:129794200-129815000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:129794200-129816800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:129794200-129824800	Weak transcription	Osteobl	bone
28	chr4:129794200-129829400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:129794400-129801200	Weak transcription	Fetal Intestine Large	intestine
30	chr4:129794400-129804000	Weak transcription	Fetal Stomach	stomach
31	chr4:129794400-129805600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:129794400-129809400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:129794400-129811000	Weak transcription	Aorta	Aorta
34	chr4:129794400-129811200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr4:129794400-129811400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:129794400-129823800	Weak transcription	Left Ventricle	heart
37	chr4:129794400-129825600	Weak transcription	Gastric	stomach
38	chr4:129794400-129860200	Weak transcription	Thymus	Thymus
39	chr4:129795000-129803400	Weak transcription	Primary B cells from cord blood	blood
40	chr4:129795000-129809400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:129795000-129824600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:129795200-129805200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:129795200-129807800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr4:129795200-129813400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr4:129795400-129809600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:129795400-129810200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:129795400-129811200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:129795600-129802000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:129795800-129803000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:129795800-129808800	Weak transcription	HUVEC	blood vessel

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