Variant report

Variant	rs10305720
Chromosome Location	chr1:150798577-150798578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150788842..150790398-chr1:150796829..150799047,2	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1027699	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10305664	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10305672	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10305673	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10305704	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10305711	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10305714	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10399947	0.85[EUR][1000 genomes]
rs10788794	0.84[EUR][1000 genomes]
rs10888391	0.84[EUR][1000 genomes]
rs10888392	0.84[EUR][1000 genomes]
rs10888394	0.86[EUR][1000 genomes]
rs10888395	0.88[EUR][1000 genomes]
rs10888398	0.86[EUR][1000 genomes]
rs11204722	0.84[EUR][1000 genomes]
rs11204726	0.86[EUR][1000 genomes]
rs11204733	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204739	0.81[EUR][1000 genomes]
rs11204747	0.81[EUR][1000 genomes]
rs11204748	0.80[EUR][1000 genomes]
rs11204749	0.81[EUR][1000 genomes]
rs11552229	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11582281	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11589458	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11589886	0.82[EUR][1000 genomes]
rs11800855	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12075597	0.82[EUR][1000 genomes]
rs12085336	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12096831	0.82[EUR][1000 genomes]
rs12097963	0.81[EUR][1000 genomes]
rs12409208	0.82[EUR][1000 genomes]
rs12410394	0.82[EUR][1000 genomes]
rs12410869	0.89[EUR][1000 genomes]
rs1532770	0.82[EUR][1000 genomes]
rs16827671	0.86[EUR][1000 genomes]
rs17660092	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1889740	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1889741	0.88[EUR][1000 genomes]
rs1972060	0.80[EUR][1000 genomes]
rs2089082	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2228099	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2256355	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271076	0.82[EUR][1000 genomes]
rs2280627	0.80[EUR][1000 genomes]
rs2864873	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2864882	0.86[EUR][1000 genomes]
rs2867297	0.81[EUR][1000 genomes]
rs36008098	0.89[EUR][1000 genomes]
rs3768013	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3768015	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3768016	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768018	0.84[EUR][1000 genomes]
rs4319334	0.81[EUR][1000 genomes]
rs4509581	0.81[EUR][1000 genomes]
rs4970931	0.82[EUR][1000 genomes]
rs4970980	0.89[EUR][1000 genomes]
rs4970982	0.82[EUR][1000 genomes]
rs4970984	0.86[EUR][1000 genomes]
rs4970985	0.86[EUR][1000 genomes]
rs57818453	0.80[EUR][1000 genomes]
rs59337856	0.86[EUR][1000 genomes]
rs6587542	0.82[EUR][1000 genomes]
rs6660084	0.86[EUR][1000 genomes]
rs6660845	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6669855	0.85[EUR][1000 genomes]
rs66847267	0.86[EUR][1000 genomes]
rs6686064	0.81[EUR][1000 genomes]
rs72704639	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72704652	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72704654	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72704656	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72704658	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72704679	0.84[EUR][1000 genomes]
rs7514004	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7521592	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7532045	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7556451	0.82[EUR][1000 genomes]
rs9661876	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv2788	chr1:150755334-150800785	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv872420	chr1:150786038-150847647	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1010875	chr1:150796816-150845827	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs10305720	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs10305720	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs10305720	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs10305720	RP11-316M1.12	cis	Thyroid	GTEx
rs10305720	GOLPH3L	cis	Nerve Tibial	GTEx
rs10305720	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs10305720	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs10305720	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs10305720	RP11-316M1.12	cis	Whole Blood	GTEx
rs10305720	RP11-316M1.12	cis	Artery Aorta	GTEx
rs10305720	HORMAD1	cis	Nerve Tibial	GTEx
rs10305720	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs10305720	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs10305720	CTSS	cis	Thyroid	GTEx
rs10305720	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs10305720	RP11-316M1.12	cis	lung	GTEx
rs10305720	HORMAD1	cis	Esophagus Mucosa	GTEx
rs10305720	RP11-316M1.12	cis	Artery Tibial	GTEx
rs10305720	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs10305720	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs10305720	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs10305720	CTSK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150782200-150809600	Strong transcription	Fetal Muscle Leg	muscle
2	chr1:150782200-150809800	Strong transcription	Stomach Smooth Muscle	stomach
3	chr1:150782200-150813000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:150782400-150812200	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr1:150782600-150802800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:150783200-150809800	Strong transcription	Fetal Thymus	thymus
7	chr1:150783200-150816600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:150783200-150816800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:150784000-150802000	Strong transcription	Fetal Lung	lung
10	chr1:150785800-150806400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:150785800-150812400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:150786000-150808600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:150788400-150808000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr1:150788400-150809800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:150788400-150812200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:150789400-150801000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:150789600-150801000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:150789800-150798800	Weak transcription	A549	lung
19	chr1:150790000-150799800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:150790000-150801400	Weak transcription	Fetal Brain Male	brain
21	chr1:150790000-150804600	Weak transcription	Pancreas	Pancrea
22	chr1:150790600-150801000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:150790600-150802400	Weak transcription	Esophagus	oesophagus
24	chr1:150790800-150811400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:150791200-150806600	Weak transcription	Small Intestine	intestine
26	chr1:150791800-150809000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:150792200-150814800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:150792400-150801800	Strong transcription	Colon Smooth Muscle	Colon
29	chr1:150792600-150803200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:150792600-150815400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:150792800-150812400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:150793000-150799000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:150793000-150816400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:150793200-150823200	Strong transcription	Placenta	Placenta
35	chr1:150793600-150815800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:150793800-150813800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:150794000-150798600	Strong transcription	Liver	Liver
38	chr1:150794000-150800000	Strong transcription	Fetal Stomach	stomach
39	chr1:150794000-150800800	Weak transcription	K562	blood
40	chr1:150794000-150805800	Strong transcription	Osteobl	bone
41	chr1:150794000-150809600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:150794000-150813600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:150794200-150798600	Weak transcription	NHEK	skin
44	chr1:150794200-150799200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:150794200-150799800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:150794200-150799800	Strong transcription	Fetal Intestine Small	intestine
47	chr1:150794200-150807800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:150794600-150812800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:150795400-150800400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:150795400-150800400	Weak transcription	Fetal Heart	heart

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