Variant report

Variant	rs10915828
Chromosome Location	chr1:225632607-225632608
allele	G/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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225624234..225625837-chr1:225632480..225634509,2	K562	blood:
2	chr1:225632160..225634552-chr1:225642936..225645932,3	K562	blood:
3	chr1:225614179..225618111-chr1:225627420..225635153,13	K562	blood:
4	chr1:225609559..225620018-chr1:225630046..225635440,23	K562	blood:
5	chr1:225631906..225634098-chr1:225666664..225668819,2	K562	blood:
6	chr1:225611259..225613937-chr1:225629471..225632737,4	K562	blood:
7	chr1:225625909..225628498-chr1:225632163..225635027,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10753406	0.88[ASN][1000 genomes]
rs10799311	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10799316	0.93[CHB][hapmap];0.83[CHD][hapmap]
rs10799317	0.83[ASN][1000 genomes]
rs10799318	0.81[ASN][1000 genomes]
rs10799319	0.81[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[YRI][hapmap]
rs10915830	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10915833	0.89[ASN][1000 genomes]
rs10915839	0.84[ASN][1000 genomes]
rs10915847	0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]
rs11584675	0.89[ASN][1000 genomes]
rs1222440	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2066233	0.83[ASW][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs2639703	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2657569	0.93[CHB][hapmap]
rs2840967	0.93[CHB][hapmap]
rs2840968	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs3820226	0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[YRI][hapmap]
rs4653637	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653639	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653643	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs487591	0.81[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs498350	0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs554744	0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs554992	0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs576861	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.89[YRI][hapmap]
rs6426076	0.91[ASN][1000 genomes]
rs6426077	0.83[ASN][1000 genomes]
rs6668770	0.86[ASN][1000 genomes]
rs6696038	0.83[CHB][hapmap]
rs6697783	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6702452	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6702538	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6702555	0.84[ASN][1000 genomes]
rs6751	0.93[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs712062	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.89[YRI][hapmap]
rs7515907	0.91[ASN][1000 genomes]
rs7515939	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524766	0.82[ASN][1000 genomes]
rs7541598	0.91[ASN][1000 genomes]
rs7549456	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7555553	0.91[ASN][1000 genomes]
rs947034	0.83[AFR][1000 genomes];0.97[ASN][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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10915828	LBR	cis	Artery Tibial	GTEx
rs10915828	C1orf95	cis	cerebellum	SCAN
rs10915828	ENAH	cis	normal skin	skin_eQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225625400-225636000	Enhancers	Colon Smooth Muscle	Colon
2	chr1:225626000-225636200	Enhancers	Fetal Intestine Large	intestine
3	chr1:225628800-225633000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:225629200-225633000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr1:225629200-225636400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:225629400-225635600	Enhancers	Primary hematopoietic stem cells	blood
7	chr1:225629400-225635600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:225629600-225634000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr1:225629600-225634200	Enhancers	Spleen	Spleen
10	chr1:225629800-225634800	Enhancers	HUVEC	blood vessel
11	chr1:225630200-225633200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:225630200-225633400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:225630200-225634600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:225630200-225635200	Enhancers	Liver	Liver
15	chr1:225630200-225636400	Enhancers	Fetal Intestine Small	intestine
16	chr1:225630800-225633800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr1:225630800-225636600	Enhancers	Fetal Muscle Leg	muscle
18	chr1:225631000-225633200	Weak transcription	Lung	lung
19	chr1:225631000-225634400	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:225631200-225633200	Weak transcription	Small Intestine	intestine
21	chr1:225631200-225633400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:225631200-225633400	Weak transcription	Gastric	stomach
23	chr1:225631200-225635000	Weak transcription	Psoas Muscle	Psoas
24	chr1:225631400-225633400	Weak transcription	Fetal Heart	heart
25	chr1:225631400-225633400	Enhancers	HepG2	liver
26	chr1:225631400-225634200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:225631600-225633800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr1:225632200-225633200	Weak transcription	Left Ventricle	heart
29	chr1:225632200-225633200	Enhancers	Rectal Smooth Muscle	rectum
30	chr1:225632200-225633200	Weak transcription	Right Ventricle	heart
31	chr1:225632200-225634000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:225632200-225634000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:225632200-225635800	Enhancers	Fetal Stomach	stomach
34	chr1:225632200-225637800	Enhancers	Stomach Mucosa	stomach
35	chr1:225632400-225632800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr1:225632400-225632800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:225632400-225632800	Active TSS	Colonic Mucosa	Colon
38	chr1:225632400-225632800	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:225632400-225632800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr1:225632400-225632800	Flanking Active TSS	Thymus	Thymus
41	chr1:225632400-225632800	Flanking Active TSS	Osteobl	bone
42	chr1:225632400-225633000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:225632400-225633000	Flanking Active TSS	Fetal Thymus	thymus
44	chr1:225632400-225633000	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr1:225632400-225633200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr1:225632400-225633200	Flanking Active TSS	K562	blood
47	chr1:225632400-225633400	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr1:225632400-225633400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:225632400-225633600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:225632400-225633600	Flanking Active TSS	Primary B cells from cord blood	blood

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