Variant report

Variant	rs4419238
Chromosome Location	chr2:113053228-113053229
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113052733..113055599-chr2:113064270..113066173,2	MCF-7	breast:
2	chr2:113033406..113035209-chr2:113052659..113055582,2	K562	blood:
3	chr2:113033709..113035506-chr2:113052735..113055582,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10167748	0.92[ASN][1000 genomes]
rs10169159	0.81[ASN][1000 genomes]
rs10175234	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10177573	0.81[ASN][1000 genomes]
rs10191002	0.96[ASN][1000 genomes]
rs10203614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203843	1.00[ASN][1000 genomes]
rs10205897	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10439391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864903	1.00[ASN][1000 genomes]
rs11123135	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123136	0.93[ASN][1000 genomes]
rs11896500	0.98[ASN][1000 genomes]
rs11903741	0.98[ASN][1000 genomes]
rs11904424	0.95[ASN][1000 genomes]
rs12464478	0.89[ASN][1000 genomes]
rs12711738	0.81[ASN][1000 genomes]
rs13387611	0.94[ASN][1000 genomes]
rs34471791	0.83[ASN][1000 genomes]
rs34623958	0.81[ASN][1000 genomes]
rs4258804	1.00[ASN][1000 genomes]
rs4299347	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4332934	1.00[ASN][1000 genomes]
rs4352239	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4392265	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4399734	0.98[ASN][1000 genomes]
rs4430968	1.00[ASN][1000 genomes]
rs4446076	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4450606	1.00[ASN][1000 genomes]
rs4450607	0.99[ASN][1000 genomes]
rs4456711	1.00[ASN][1000 genomes]
rs4507112	0.96[ASN][1000 genomes]
rs4522611	0.96[ASN][1000 genomes]
rs4525706	0.96[ASN][1000 genomes]
rs4539797	1.00[ASN][1000 genomes]
rs4542853	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4578863	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4622729	0.96[ASN][1000 genomes]
rs4630773	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4849058	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58337061	1.00[ASN][1000 genomes]
rs62160223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542050	0.81[ASN][1000 genomes]
rs6542051	1.00[ASN][1000 genomes]
rs6542052	0.87[ASN][1000 genomes]
rs6542053	0.96[ASN][1000 genomes]
rs6542054	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6706874	0.81[ASN][1000 genomes]
rs6708164	0.93[ASN][1000 genomes]
rs6716010	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6725933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726412	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6733138	0.96[ASN][1000 genomes]
rs6744364	0.94[ASN][1000 genomes]
rs6745942	0.81[ASN][1000 genomes]
rs6751146	0.96[ASN][1000 genomes]
rs6758110	0.96[ASN][1000 genomes]
rs6761599	0.96[ASN][1000 genomes]
rs71414636	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72831684	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7557862	0.96[ASN][1000 genomes]
rs7564052	1.00[ASN][1000 genomes]
rs7569894	0.96[ASN][1000 genomes]
rs7579561	0.94[ASN][1000 genomes]
rs7591439	0.94[ASN][1000 genomes]
rs7598168	0.97[ASN][1000 genomes]
rs7599041	0.92[ASN][1000 genomes]
rs7600338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601200	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7601888	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8179708	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv874868	chr2:113021811-113076095	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv874872	chr2:113027569-113070889	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv874873	chr2:113027569-113083367	Active TSS Weak transcription Flanking Active TSS Enhancers 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	33 gene(s)	inside rSNPs	diseases
12	nsv874874	chr2:113027569-113089267	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv874875	chr2:113038409-113070889	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv874876	chr2:113051291-113089267	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4419238	RGPD8	cis	Nerve Tibial	GTEx
rs4419238	RGPD8	cis	Artery Tibial	GTEx
rs4419238	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs4419238	RGPD8	cis	lung	GTEx
rs4419238	RGPD8	cis	Muscle Skeletal	GTEx
rs4419238	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113034200-113058200	Weak transcription	Ovary	ovary
2	chr2:113034400-113097000	Weak transcription	Psoas Muscle	Psoas
3	chr2:113035000-113057800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:113035000-113057800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:113035000-113057800	Weak transcription	Fetal Intestine Small	intestine
6	chr2:113035600-113058200	Weak transcription	Primary B cells from cord blood	blood
7	chr2:113035800-113058000	Weak transcription	Primary T cells from cord blood	blood
8	chr2:113035800-113060400	Weak transcription	Fetal Thymus	thymus
9	chr2:113035800-113067400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:113036600-113058000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:113037000-113054200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:113040000-113081800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:113040600-113054400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:113041200-113058600	Weak transcription	Fetal Heart	heart
15	chr2:113041400-113058600	Weak transcription	K562	blood
16	chr2:113046200-113057800	Weak transcription	Thymus	Thymus
17	chr2:113046600-113079800	Weak transcription	Fetal Stomach	stomach
18	chr2:113046800-113065000	Weak transcription	HSMMtube	muscle
19	chr2:113047200-113058200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:113047600-113058400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:113048000-113084400	Weak transcription	Fetal Kidney	kidney
22	chr2:113048200-113064200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:113048400-113061000	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:113048600-113060800	Weak transcription	Brain Substantia Nigra	brain
25	chr2:113048600-113081600	Weak transcription	Brain Anterior Caudate	brain
26	chr2:113048600-113081800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:113049000-113054200	Weak transcription	Liver	Liver
28	chr2:113050400-113057800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:113050600-113090600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:113051000-113088600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:113051600-113053400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:113051600-113058200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:113051600-113061800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:113051600-113080600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:113051600-113081800	Weak transcription	Spleen	Spleen
36	chr2:113051600-113088600	Weak transcription	Esophagus	oesophagus
37	chr2:113051800-113057800	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:113051800-113057800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:113051800-113060600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:113051800-113065000	Weak transcription	Left Ventricle	heart
41	chr2:113051800-113081800	Weak transcription	Gastric	stomach
42	chr2:113051800-113081800	Weak transcription	Lung	lung
43	chr2:113052000-113054400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:113052000-113058200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:113052000-113062000	Weak transcription	Aorta	Aorta
46	chr2:113052200-113053400	Enhancers	Adipose Nuclei	Adipose
47	chr2:113052200-113060800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:113052800-113058000	Weak transcription	Osteobl	bone
49	chr2:113053000-113053400	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr2:113053200-113053400	Enhancers	Brain Angular Gyrus	brain

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