Variant report

Variant	rs35721448
Chromosome Location	chr17:45134012-45134013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPRML-3	chr17:45133975-45134119	ENSG00000262879.1
2	lnc-GOSR2-2	chr17:45131884-45134124	NONHSAT054246

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10514915	0.93[ASN][1000 genomes]
rs11079748	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079750	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079752	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11649887	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654517	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658350	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11871052	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11871364	0.82[EUR][1000 genomes]
rs12603447	0.93[ASN][1000 genomes]
rs12939753	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12942936	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12949929	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12950276	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12950699	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1634260	0.93[ASN][1000 genomes]
rs2007723	0.91[ASN][1000 genomes]
rs2316331	0.91[ASN][1000 genomes]
rs2317376	0.93[ASN][1000 genomes]
rs2873131	0.93[ASN][1000 genomes]
rs34038545	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34314554	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34710835	0.98[ASN][1000 genomes]
rs4074247	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4074249	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968253	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968301	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4968304	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56362502	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7207418	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7214785	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215573	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7215903	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7215907	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7219544	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7219899	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7220777	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7222781	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8077021	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889451	0.93[ASN][1000 genomes]
rs9899078	0.93[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	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv9565	chr17:45088304-45135259	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv962331	chr17:45088443-45141744	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	esv1843358	chr17:45090768-45141959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	esv1851648	chr17:45091619-45146146	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	esv1846431	chr17:45092987-45145946	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
14	nsv820424	chr17:45114979-45135615	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
15	esv19725	chr17:45115875-45135615	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
17	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
18	esv16013	chr17:45125753-45134686	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv21010	chr17:45125753-45177221	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers 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	8 gene(s)	inside rSNPs	diseases
20	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
21	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35721448	GOSR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45121400-45142200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr17:45123800-45143600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr17:45125200-45143600	Weak transcription	HepG2	liver
4	chr17:45125400-45143800	Weak transcription	NHLF	lung
5	chr17:45128200-45140000	Weak transcription	K562	blood
6	chr17:45128200-45143600	Weak transcription	HSMMtube	muscle
7	chr17:45128200-45143800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr17:45128600-45134200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:45128800-45143600	Weak transcription	HUVEC	blood vessel
10	chr17:45128800-45144600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:45129200-45137200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr17:45129400-45144200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:45129600-45134200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:45129600-45134200	Strong transcription	Fetal Stomach	stomach
15	chr17:45129600-45134200	Strong transcription	Thymus	Thymus
16	chr17:45129600-45134400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr17:45129600-45135600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:45129800-45134200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:45129800-45134400	Strong transcription	Fetal Intestine Large	intestine
20	chr17:45129800-45135400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:45129800-45144000	Weak transcription	Hela-S3	cervix
22	chr17:45130000-45144200	Weak transcription	Primary B cells from cord blood	blood
23	chr17:45130200-45134200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr17:45130200-45134200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:45130200-45134200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr17:45130200-45135000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:45130600-45134200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr17:45130600-45143800	Weak transcription	NHEK	skin
29	chr17:45130800-45141600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:45131200-45143600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr17:45131200-45144000	Weak transcription	Brain Germinal Matrix	brain
32	chr17:45131400-45142000	Weak transcription	NHDF-Ad	bronchial
33	chr17:45131600-45143600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr17:45131800-45137200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:45131800-45141600	Weak transcription	Aorta	Aorta
36	chr17:45131800-45141600	Weak transcription	A549	lung
37	chr17:45131800-45143600	Weak transcription	HSMM	muscle
38	chr17:45131800-45144600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr17:45132000-45135600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr17:45132000-45141600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr17:45132000-45144600	Weak transcription	Spleen	Spleen
42	chr17:45132200-45141600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr17:45132200-45142800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr17:45132200-45143600	Weak transcription	Psoas Muscle	Psoas
45	chr17:45132600-45134200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr17:45132600-45143600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr17:45132600-45143600	Weak transcription	Osteobl	bone
48	chr17:45132600-45143800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr17:45132600-45144000	Weak transcription	HMEC	breast
50	chr17:45132600-45144200	Weak transcription	Colonic Mucosa	Colon

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