Variant report

Variant	rs4871825
Chromosome Location	chr8:121034642-121034643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:41753456..41755944-chr8:121034232..121035830,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235123	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10087551	0.97[ASN][1000 genomes]
rs10505376	0.90[JPT][hapmap]
rs10808506	0.90[JPT][hapmap]
rs11780985	0.90[JPT][hapmap]
rs11986346	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11996625	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12386849	0.97[ASN][1000 genomes]
rs12542032	0.97[ASN][1000 genomes]
rs12545676	0.81[ASN][1000 genomes]
rs12547479	0.97[ASN][1000 genomes]
rs12548223	1.00[JPT][hapmap]
rs1401811	0.97[ASN][1000 genomes]
rs1519812	0.88[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1519813	0.84[GIH][hapmap]
rs16893478	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs17226296	0.90[JPT][hapmap]
rs17822044	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs1973732	1.00[ASN][1000 genomes]
rs1980228	0.88[CEU][hapmap]
rs2326431	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875931	0.90[JPT][hapmap]
rs4871717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4871718	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4871720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60717250	0.81[ASN][1000 genomes]
rs6469895	0.90[JPT][hapmap]
rs66608823	0.97[ASN][1000 genomes]
rs67282053	0.93[ASN][1000 genomes]
rs7007998	0.90[JPT][hapmap]
rs72673678	0.91[ASN][1000 genomes]
rs7813041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7817522	0.97[ASN][1000 genomes]
rs7822662	0.90[JPT][hapmap]
rs7829101	0.88[CEU][hapmap];0.80[GIH][hapmap]
rs7829116	0.90[JPT][hapmap]
rs7841621	0.90[JPT][hapmap]
rs7843503	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs960887	0.84[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9656934	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv891419	chr8:120990455-121047798	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3348294	chr8:121000288-121250984	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4871825	RP11-760H22.2	cis	Adipose Subcutaneous	GTEx
rs4871825	DEPDC6	cis	uninvolved skin	skin_eQTL
rs4871825	FER1L6	cis	cerebellum	SCAN
rs4871825	DSCC1	cis	parietal	SCAN
rs4871825	DEPDC6	cis	normal skin	skin_eQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120995600-121038400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr8:121004000-121048000	Weak transcription	Stomach Mucosa	stomach
3	chr8:121004600-121041400	Weak transcription	Brain Angular Gyrus	brain
4	chr8:121005200-121045800	Weak transcription	Psoas Muscle	Psoas
5	chr8:121017000-121067000	Weak transcription	Brain Anterior Caudate	brain
6	chr8:121017800-121042000	Weak transcription	Fetal Kidney	kidney
7	chr8:121019000-121042000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr8:121020000-121044800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr8:121020000-121046000	Weak transcription	Esophagus	oesophagus
10	chr8:121021600-121038000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:121021600-121042000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr8:121022200-121048200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr8:121022400-121065400	Weak transcription	Left Ventricle	heart
14	chr8:121022800-121053000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr8:121026400-121036000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr8:121028000-121043800	Weak transcription	Liver	Liver
17	chr8:121029800-121048400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr8:121030600-121037000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr8:121030800-121035400	Strong transcription	Fetal Intestine Small	intestine
20	chr8:121030800-121035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr8:121031200-121036200	Weak transcription	Spleen	Spleen
22	chr8:121032000-121039600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr8:121032000-121041800	Weak transcription	Brain Substantia Nigra	brain
24	chr8:121032000-121058000	Weak transcription	Pancreas	Pancrea
25	chr8:121032200-121035200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr8:121032200-121036800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr8:121032200-121036800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr8:121032200-121041800	Weak transcription	Brain Hippocampus Middle	brain
29	chr8:121032200-121041800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr8:121032200-121044800	Weak transcription	Gastric	stomach
31	chr8:121032400-121036600	Weak transcription	Fetal Intestine Large	intestine
32	chr8:121032400-121044800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr8:121033000-121034800	Weak transcription	Ovary	ovary
34	chr8:121033000-121036000	Weak transcription	Fetal Muscle Leg	muscle
35	chr8:121033000-121046200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr8:121033800-121039400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr8:121034400-121035800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr8:121034400-121036800	Weak transcription	Fetal Stomach	stomach
39	chr8:121034600-121039000	Enhancers	Colon Smooth Muscle	Colon

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