Variant report

Variant	rs35871059
Chromosome Location	chr3:42701694-42701695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42693324..42695216-chr3:42700072..42702167,2	MCF-7	breast:
2	chr3:42700054..42702957-chr3:42774515..42776215,2	K562	blood:
3	chr3:42639395..42643636-chr3:42699754..42702498,4	K562	blood:
4	chr3:42695218..42698513-chr3:42700428..42704457,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114853	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000244607	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs13064597	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072295	0.82[EUR][1000 genomes]
rs13085143	1.00[ASN][1000 genomes]
rs13085695	0.82[EUR][1000 genomes]
rs13089845	0.82[EUR][1000 genomes]
rs13090902	0.82[EUR][1000 genomes]
rs13093680	0.82[EUR][1000 genomes]
rs13095447	0.82[EUR][1000 genomes]
rs13100261	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030458	0.97[EUR][1000 genomes]
rs17074662	0.82[EUR][1000 genomes]
rs17074673	0.82[EUR][1000 genomes]
rs17074674	0.82[EUR][1000 genomes]
rs17074693	0.82[EUR][1000 genomes]
rs2284303	0.82[EUR][1000 genomes]
rs2284304	0.82[EUR][1000 genomes]
rs2300057	0.82[EUR][1000 genomes]
rs2300058	0.82[EUR][1000 genomes]
rs2302352	0.82[EUR][1000 genomes]
rs33969824	0.82[EUR][1000 genomes]
rs339705	0.89[EUR][1000 genomes]
rs33984028	0.82[EUR][1000 genomes]
rs34077739	1.00[ASN][1000 genomes]
rs34196076	1.00[ASN][1000 genomes]
rs34243788	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683820	0.82[EUR][1000 genomes]
rs34687113	0.80[EUR][1000 genomes]
rs34762478	0.82[EUR][1000 genomes]
rs34801786	0.82[EUR][1000 genomes]
rs34852409	0.82[EUR][1000 genomes]
rs34977988	0.82[EUR][1000 genomes]
rs35216140	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384559	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35676838	0.82[EUR][1000 genomes]
rs35890296	0.82[EUR][1000 genomes]
rs36033201	0.82[EUR][1000 genomes]
rs36043081	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774401	0.82[EUR][1000 genomes]
rs3774402	0.82[EUR][1000 genomes]
rs3774404	0.82[EUR][1000 genomes]
rs3774407	0.82[EUR][1000 genomes]
rs3846058	0.82[EUR][1000 genomes]
rs3846059	0.82[EUR][1000 genomes]
rs3856737	0.82[EUR][1000 genomes]
rs3900780	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	1.00[ASN][1000 genomes]
rs55994846	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047094	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56797870	0.82[EUR][1000 genomes]
rs57259216	0.82[EUR][1000 genomes]
rs58645732	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58868911	0.82[EUR][1000 genomes]
rs59914338	0.82[EUR][1000 genomes]
rs60232916	0.82[EUR][1000 genomes]
rs60348477	0.82[EUR][1000 genomes]
rs60535002	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61149998	0.82[EUR][1000 genomes]
rs6441928	0.82[EUR][1000 genomes]
rs66786953	0.81[EUR][1000 genomes]
rs66933062	1.00[ASN][1000 genomes]
rs67059259	0.82[EUR][1000 genomes]
rs67174294	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67533173	0.80[EUR][1000 genomes]
rs67583158	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771105	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778982	0.82[EUR][1000 genomes]
rs6782164	0.82[EUR][1000 genomes]
rs67832425	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788548	0.82[EUR][1000 genomes]
rs6790204	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6793186	0.82[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6795296	0.82[EUR][1000 genomes]
rs6797491	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797545	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004576	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68028490	0.82[EUR][1000 genomes]
rs68071013	0.82[EUR][1000 genomes]
rs71323162	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864022	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864072	0.82[EUR][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616701	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617403	0.82[EUR][1000 genomes]
rs7617736	0.82[EUR][1000 genomes]
rs7623867	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7624628	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35871059	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42697000-42702400	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr3:42697200-42703000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:42697200-42704600	Weak transcription	Primary B cells from cord blood	blood
4	chr3:42697400-42702000	Weak transcription	Fetal Kidney	kidney
5	chr3:42697400-42703000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:42697400-42706800	Weak transcription	HMEC	breast
7	chr3:42697400-42708800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:42697400-42708800	Weak transcription	Fetal Lung	lung
9	chr3:42697600-42703400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:42697600-42704600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:42697600-42704800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:42697600-42707000	Weak transcription	A549	lung
13	chr3:42697600-42708000	Weak transcription	Colonic Mucosa	Colon
14	chr3:42697600-42709800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:42697800-42702200	Weak transcription	HSMMtube	muscle
16	chr3:42697800-42702600	Genic enhancers	Brain Hippocampus Middle	brain
17	chr3:42697800-42707200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:42697800-42707600	Strong transcription	Fetal Intestine Small	intestine
19	chr3:42697800-42707800	Weak transcription	Psoas Muscle	Psoas
20	chr3:42697800-42709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:42698000-42706400	Strong transcription	Fetal Stomach	stomach
22	chr3:42698200-42706600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:42698200-42708000	Weak transcription	HSMM	muscle
24	chr3:42698200-42708400	Weak transcription	HUVEC	blood vessel
25	chr3:42698400-42703800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:42698400-42704000	Genic enhancers	Right Ventricle	heart
27	chr3:42698600-42703200	Genic enhancers	Stomach Smooth Muscle	stomach
28	chr3:42698800-42703400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:42699200-42702400	Strong transcription	Fetal Intestine Large	intestine
30	chr3:42699200-42702600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:42699400-42702000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:42699400-42703200	Enhancers	Fetal Heart	heart
33	chr3:42699400-42703400	Strong transcription	NHEK	skin
34	chr3:42699600-42701800	Genic enhancers	Left Ventricle	heart
35	chr3:42699600-42702200	Genic enhancers	Brain Cingulate Gyrus	brain
36	chr3:42699800-42702600	Genic enhancers	Brain Anterior Caudate	brain
37	chr3:42699800-42703800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:42699800-42704800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:42699800-42705000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:42699800-42705600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr3:42699800-42706800	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr3:42700000-42702000	Enhancers	Right Atrium	heart
43	chr3:42700000-42702600	Genic enhancers	Brain Inferior Temporal Lobe	brain
44	chr3:42700000-42707000	Weak transcription	HepG2	liver
45	chr3:42700200-42701800	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr3:42700200-42702000	Enhancers	Colon Smooth Muscle	Colon
47	chr3:42700200-42702200	Genic enhancers	Gastric	stomach
48	chr3:42700200-42702600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:42700200-42702600	Genic enhancers	Brain Substantia Nigra	brain
50	chr3:42700200-42704600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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