Variant report

Variant	rs2716117
Chromosome Location	chr1:59376937-59376938
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59249350..59250973-chr1:59375255..59376962,2	K562	blood:
2	chr1:59370025..59373918-chr1:59374367..59377851,5	K562	blood:
3	chr1:59280903..59282902-chr1:59376197..59378473,2	MCF-7	breast:
4	chr1:59375398..59378339-chr1:59379792..59381742,2	K562	blood:
5	chr1:59246784..59250688-chr1:59376350..59380858,6	K562	blood:

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12401645	1.00[TSI][hapmap]
rs17118446	1.00[TSI][hapmap]
rs1886745	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2492321	0.98[LWK][hapmap];0.81[MKK][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs2716132	1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2716161	0.80[ASW][hapmap];0.87[LWK][hapmap]
rs2764903	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2764905	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2764906	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2764908	0.80[ASW][hapmap];0.82[AFR][1000 genomes]
rs2999129	0.80[ASW][hapmap];0.86[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59369800-59388200	Weak transcription	Gastric	stomach
2	chr1:59370000-59377800	Weak transcription	Aorta	Aorta
3	chr1:59370200-59377200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:59370200-59377600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:59370600-59377400	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:59370600-59377400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:59372200-59377400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:59373400-59377400	Weak transcription	K562	blood
9	chr1:59373400-59378000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:59374200-59379800	Enhancers	Fetal Intestine Large	intestine
11	chr1:59374400-59379800	Enhancers	Fetal Intestine Small	intestine
12	chr1:59374800-59377800	Enhancers	Stomach Mucosa	stomach
13	chr1:59375000-59377400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:59375400-59377200	Enhancers	Small Intestine	intestine
15	chr1:59375800-59379400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:59375800-59380600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:59376000-59377400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:59376200-59377200	Weak transcription	HUVEC	blood vessel
19	chr1:59376200-59378000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr1:59376400-59379200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:59376800-59377600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr1:59376800-59378400	Enhancers	Duodenum Mucosa	Duodenum

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