Variant report

Variant	rs17002978
Chromosome Location	chr4:79073700-79073701
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10008346	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10009577	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014790	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020175	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10026071	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027675	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029277	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032397	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10222691	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10222693	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10440393	0.98[EUR][1000 genomes]
rs10518187	0.93[EUR][1000 genomes]
rs17002926	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002927	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002937	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002965	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002971	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002972	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453030	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28433896	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437781	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438642	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28624340	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627481	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640590	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867009	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673365	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28728167	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28794638	0.95[EUR][1000 genomes]
rs28825502	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859895	1.00[CHB][hapmap]
rs56069998	0.98[EUR][1000 genomes]
rs56209110	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56346346	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56404216	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533375	1.00[CHB][hapmap]
rs72860675	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72860700	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284616	1.00[CHB][hapmap]
rs9284617	1.00[CHB][hapmap]
rs9307350	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv879502	chr4:79052851-79144309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17002978	SNX7	trans	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79067200-79078000	Weak transcription	Psoas Muscle	Psoas
2	chr4:79069800-79074400	Enhancers	Fetal Intestine Large	intestine
3	chr4:79069800-79074400	Enhancers	Fetal Intestine Small	intestine
4	chr4:79071000-79083600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:79071200-79075200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:79071200-79078000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:79071200-79082600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:79071400-79075400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:79071400-79075600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:79071400-79077200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:79071400-79078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:79071400-79096600	Weak transcription	Pancreas	Pancrea
13	chr4:79071600-79076600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:79072000-79073800	Weak transcription	Fetal Heart	heart
15	chr4:79072000-79076800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:79072600-79076000	Enhancers	HepG2	liver
17	chr4:79072800-79076000	Weak transcription	Fetal Lung	lung
18	chr4:79073200-79073800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:79073200-79074400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr4:79073200-79076800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:79073400-79073800	Weak transcription	Fetal Kidney	kidney
22	chr4:79073400-79074400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:79073400-79076000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:79073400-79076800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:79073600-79075200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:79073600-79082000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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