Variant report

Variant	rs10788799
Chromosome Location	chr1:151072864-151072865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150996791..150997291-chr1:151072097..151072918,2	MCF-7	breast:
2	chr1:151072449..151072961-chr1:151118250..151119246,2	MCF-7	breast:
3	chr1:151072366..151073004-chr1:151224013..151224543,2	MCF-7	breast:
4	chr1:151070659..151073129-chr1:151227300..151229103,2	K562	blood:
5	chr1:151072083..151072933-chr1:151128224..151129166,3	MCF-7	breast:
6	chr1:151022097..151024795-chr1:151070842..151073434,2	K562	blood:
7	chr1:151071098..151073489-chr1:151128242..151129745,2	K562	blood:
8	chr1:151071939..151072878-chr1:151128175..151129386,8	K562	blood:
9	chr1:151071447..151073068-chr1:151128034..151129071,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143363	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10788798	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204777	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204778	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204779	0.83[EUR][1000 genomes]
rs11204780	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12039334	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12039542	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12040729	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12117163	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1524773	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2140709	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2902810	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3738481	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3806386	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3806387	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4970939	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4970993	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4970998	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4970999	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971000	0.80[AFR][1000 genomes]
rs4971002	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971003	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971005	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971006	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971007	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971008	0.87[EUR][1000 genomes]
rs5023311	0.87[EUR][1000 genomes]
rs61819199	0.80[AFR][1000 genomes]
rs6587553	0.84[EUR][1000 genomes]
rs6668894	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6694158	0.81[EUR][1000 genomes]
rs6697617	0.83[EUR][1000 genomes]
rs7366148	0.81[AMR][1000 genomes];0.82[EUR][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	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
2	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
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872421	chr1:151055670-151098077	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10788799	BNIPL	cis	lung	GTEx
rs10788799	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs10788799	BNIPL	cis	Thyroid	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151044000-151079600	Weak transcription	Spleen	Spleen
2	chr1:151044000-151080600	Weak transcription	Esophagus	oesophagus
3	chr1:151044200-151080200	Weak transcription	Aorta	Aorta
4	chr1:151044400-151079000	Weak transcription	Left Ventricle	heart
5	chr1:151044400-151079600	Weak transcription	Lung	lung
6	chr1:151044400-151090200	Weak transcription	Gastric	stomach
7	chr1:151044400-151090400	Weak transcription	Right Ventricle	heart
8	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
9	chr1:151044600-151076000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:151044600-151080400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:151044600-151080600	Weak transcription	Brain Anterior Caudate	brain
12	chr1:151044600-151081000	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:151044800-151079600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:151044800-151080200	Weak transcription	Fetal Brain Female	brain
15	chr1:151044800-151089400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:151044800-151098800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:151045000-151079400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:151045000-151080000	Weak transcription	Brain Angular Gyrus	brain
19	chr1:151045000-151080400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:151045200-151081000	Weak transcription	Placenta	Placenta
21	chr1:151047200-151090400	Weak transcription	Dnd41	blood
22	chr1:151047400-151090400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:151047600-151075200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:151047800-151079600	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:151047800-151089200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:151052200-151103000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:151056200-151079600	Weak transcription	Primary B cells from cord blood	blood
28	chr1:151057800-151075200	Weak transcription	Psoas Muscle	Psoas
29	chr1:151060600-151090200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:151061400-151079200	Weak transcription	Osteobl	bone
31	chr1:151061800-151090400	Weak transcription	Fetal Kidney	kidney
32	chr1:151061800-151105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:151062000-151079400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:151062200-151088800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:151062400-151076000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:151063200-151074200	Weak transcription	Liver	Liver
37	chr1:151063200-151080800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:151063400-151079600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:151064200-151079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:151064200-151103400	Weak transcription	Colonic Mucosa	Colon
41	chr1:151064400-151079600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:151065800-151077600	Weak transcription	Thymus	Thymus
43	chr1:151067000-151103400	Weak transcription	Fetal Brain Male	brain
44	chr1:151067800-151079400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:151068000-151075200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:151068000-151079400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:151068400-151075200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:151068400-151075200	Weak transcription	Ovary	ovary
49	chr1:151068400-151090400	Weak transcription	Pancreas	Pancrea
50	chr1:151068600-151079600	Weak transcription	Brain Germinal Matrix	brain

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