Variant report

Variant	rs346502
Chromosome Location	chr4:86857403-86857404
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:86855497..86859080-chr4:86873833..86876584,3	MCF-7	breast:
2	chr4:86851168..86853730-chr4:86855449..86857714,2	K562	blood:
3	chr4:86855216..86857997-chr4:86860601..86862726,2	K562	blood:
4	chr4:86853756..86855558-chr4:86856892..86859472,2	K562	blood:

Variant related genes	Relation type
ENSG00000138639	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11724681	0.91[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs168308	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs173201	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs182961	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2164535	0.83[EUR][1000 genomes]
rs2164536	0.84[EUR][1000 genomes]
rs2164537	0.84[EUR][1000 genomes]
rs2575680	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2589504	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2589509	0.84[EUR][1000 genomes]
rs2665877	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346467	0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346471	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs346475	0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs346478	0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346480	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346484	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346485	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346488	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346492	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346498	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs346503	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs346504	0.95[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs346505	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346506	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346507	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6851229	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs958860	0.84[EUR][1000 genomes]
rs958861	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879519	chr4:86786204-86871282	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86851200-86863200	Weak transcription	Psoas Muscle	Psoas
2	chr4:86851400-86861600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr4:86851400-86865800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:86851400-86874600	Weak transcription	HSMMtube	muscle
5	chr4:86851600-86858200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:86851600-86870000	Weak transcription	HSMM	muscle
7	chr4:86851600-86874800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:86853800-86860000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:86853800-86864400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:86854000-86867400	Weak transcription	Fetal Lung	lung
11	chr4:86854000-86874200	Weak transcription	Fetal Stomach	stomach
12	chr4:86854000-86893000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr4:86854200-86859000	Weak transcription	Fetal Intestine Large	intestine
14	chr4:86854200-86859000	Weak transcription	Fetal Intestine Small	intestine
15	chr4:86854200-86859200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:86854200-86859200	Weak transcription	Aorta	Aorta
17	chr4:86854200-86860000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:86854200-86860200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:86854200-86860200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:86854200-86860200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:86854200-86863000	Weak transcription	HUVEC	blood vessel
22	chr4:86854200-86863200	Weak transcription	Pancreas	Pancrea
23	chr4:86854200-86880200	Weak transcription	Gastric	stomach
24	chr4:86854200-86893000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
26	chr4:86854400-86858400	Weak transcription	A549	lung
27	chr4:86854400-86860800	Weak transcription	Adipose Nuclei	Adipose
28	chr4:86854600-86859000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:86854600-86859000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:86854600-86863000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:86854800-86863200	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:86855000-86859200	Weak transcription	NHDF-Ad	bronchial
33	chr4:86855200-86858800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:86855400-86858000	Weak transcription	Liver	Liver
35	chr4:86855600-86858000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:86855600-86858600	Weak transcription	Stomach Mucosa	stomach
37	chr4:86856000-86860200	Strong transcription	Primary B cells from cord blood	blood
38	chr4:86856000-86863200	Weak transcription	Right Atrium	heart
39	chr4:86857000-86858000	Weak transcription	Fetal Kidney	kidney

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