Variant report

Variant	rs17135916
Chromosome Location	chr7:102552997-102552998
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10487281	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10487284	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11496066	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12113073	1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs12113759	1.00[CHB][hapmap]
rs17135875	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17135913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474893	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2041094	1.00[CHB][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs2228687	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2411061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs3893651	1.00[ASN][1000 genomes]
rs4377880	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4398822	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4610658	1.00[CHB][hapmap]
rs55681588	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55781834	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849741	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55851590	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56314487	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336567	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56692051	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465886	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6465887	0.86[CEU][hapmap]
rs66712128	0.88[EUR][1000 genomes]
rs6955064	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965463	0.84[CEU][hapmap]
rs6968036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727175	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73192015	1.00[ASN][1000 genomes]
rs73192019	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192025	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73192026	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73714541	0.88[EUR][1000 genomes]
rs7777217	0.84[CEU][hapmap]
rs7779854	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781557	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7798582	0.88[EUR][1000 genomes]
rs7809047	1.00[CHB][hapmap];1.00[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	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17135916	LRRC17	cis	Stomach	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:102538400-102553200	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:102539200-102553000	Weak transcription	Right Atrium	heart
4	chr7:102547200-102554800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:102548200-102558000	Weak transcription	Pancreas	Pancrea
6	chr7:102549200-102553200	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:102549400-102553400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:102549800-102553000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:102549800-102553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:102550600-102553200	Weak transcription	Fetal Intestine Small	intestine
11	chr7:102550600-102553400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:102551000-102553200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:102551000-102553600	Weak transcription	Gastric	stomach
14	chr7:102551400-102553200	Weak transcription	Left Ventricle	heart
15	chr7:102551600-102554600	Strong transcription	K562	blood
16	chr7:102552200-102553200	Enhancers	HSMM	muscle
17	chr7:102552400-102553000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr7:102552400-102553000	Enhancers	Fetal Muscle Leg	muscle
19	chr7:102552600-102553000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr7:102552600-102553000	Enhancers	Psoas Muscle	Psoas
21	chr7:102552600-102553000	Enhancers	HSMMtube	muscle
22	chr7:102552600-102553200	Enhancers	Fetal Kidney	kidney
23	chr7:102552600-102553200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr7:102552600-102553200	Enhancers	HUVEC	blood vessel
25	chr7:102552800-102553000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:102552800-102553000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:102552800-102553000	Enhancers	Fetal Stomach	stomach
28	chr7:102552800-102553000	Enhancers	NH-A	brain
29	chr7:102552800-102553000	Enhancers	Osteobl	bone
30	chr7:102552800-102553200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:102552800-102553200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr7:102552800-102553200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr7:102552800-102553200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr7:102552800-102553200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr7:102552800-102553200	Enhancers	Fetal Thymus	thymus
36	chr7:102552800-102556200	Active TSS	Fetal Lung	lung
37	chr7:102552800-102556800	Active TSS	Ovary	ovary

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