Variant report

Variant	rs1805841
Chromosome Location	chr8:90992670-90992671
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90766360..90773428-chr8:90991217..91000142,22	MCF-7	breast:
2	chr8:90984874..90987349-chr8:90988956..90993202,5	MCF-7	breast:
3	chr8:90766719..90773256-chr8:90991979..90999179,19	MCF-7	breast:
4	chr8:90984484..90993091-chr8:90993260..90998893,16	MCF-7	breast:
5	chr8:90991149..90993502-chr8:91207366..91210281,2	K562	blood:

Variant related genes	Relation type
ENSG00000104320	Chromatin interaction
ENSG00000251136	Chromatin interaction
ENSG00000104312	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10095826	0.84[CEU][hapmap]
rs10100369	0.80[CEU][hapmap]
rs10109454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1061302	0.82[EUR][1000 genomes]
rs1063045	0.82[EUR][1000 genomes]
rs10956375	0.81[EUR][1000 genomes]
rs10956427	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12550313	0.82[EUR][1000 genomes]
rs12677527	0.81[EUR][1000 genomes]
rs12680903	0.81[EUR][1000 genomes]
rs13275276	0.82[EUR][1000 genomes]
rs13278453	0.82[EUR][1000 genomes]
rs13312842	0.82[EUR][1000 genomes]
rs13312935	0.82[EUR][1000 genomes]
rs1476590	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1805786	0.82[EUR][1000 genomes]
rs1805788	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1805789	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs1805790	0.82[EUR][1000 genomes]
rs1805791	0.83[EUR][1000 genomes]
rs1805792	0.84[EUR][1000 genomes]
rs1805793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805794	0.84[EUR][1000 genomes]
rs1805795	0.84[EUR][1000 genomes]
rs1805796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805797	0.82[EUR][1000 genomes]
rs1805799	0.81[EUR][1000 genomes]
rs1805800	0.81[EUR][1000 genomes]
rs1805801	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1805802	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805803	0.80[EUR][1000 genomes]
rs1805806	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1805807	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805809	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805817	0.82[EUR][1000 genomes]
rs1805818	0.82[EUR][1000 genomes]
rs1805833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805844	0.80[EUR][1000 genomes]
rs1805864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1805868	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805869	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805871	0.84[CEU][hapmap];0.96[YRI][hapmap]
rs1805889	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1881469	0.82[JPT][hapmap]
rs2073635	0.81[EUR][1000 genomes]
rs2097825	0.80[CEU][hapmap]
rs2107466	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2189618	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2189619	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2234744	0.82[EUR][1000 genomes]
rs2246157	0.82[JPT][hapmap]
rs2280780	0.82[EUR][1000 genomes]
rs2293774	0.82[EUR][1000 genomes]
rs2293775	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2308962	0.82[EUR][1000 genomes]
rs2339025	0.84[EUR][1000 genomes]
rs2697674	0.81[JPT][hapmap]
rs2697675	0.81[JPT][hapmap]
rs2734823	0.82[JPT][hapmap]
rs3026265	0.82[EUR][1000 genomes]
rs3736639	0.82[EUR][1000 genomes]
rs3758146	0.84[CEU][hapmap]
rs4961165	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4961168	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4961169	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6470522	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6470523	0.82[EUR][1000 genomes]
rs6470524	0.80[EUR][1000 genomes]
rs6987873	0.82[EUR][1000 genomes]
rs6990969	0.82[EUR][1000 genomes]
rs6991811	0.81[EUR][1000 genomes]
rs7006322	0.82[EUR][1000 genomes]
rs7010210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7018118	0.80[EUR][1000 genomes]
rs709816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs741777	0.82[EUR][1000 genomes]
rs7463645	0.84[EUR][1000 genomes]
rs7822272	0.80[CEU][hapmap]
rs7829246	0.82[EUR][1000 genomes]
rs7832009	0.84[EUR][1000 genomes]
rs867185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650098	0.82[EUR][1000 genomes]
rs9792335	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891183	chr8:90975550-91111193	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	esv2752578	chr8:90990091-90995971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1805841	NBN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90915800-90995000	Weak transcription	Fetal Brain Male	brain
2	chr8:90927800-90996000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:90962000-90994400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:90962000-90995000	Weak transcription	Aorta	Aorta
5	chr8:90970800-90993200	Weak transcription	Psoas Muscle	Psoas
6	chr8:90971000-90994000	Weak transcription	Brain Substantia Nigra	brain
7	chr8:90971200-90994400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr8:90971400-90993800	Weak transcription	Small Intestine	intestine
9	chr8:90971800-90995600	Weak transcription	Right Ventricle	heart
10	chr8:90973800-90993800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr8:90974200-90993800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr8:90975600-90993800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr8:90975600-90993800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr8:90975600-90994000	Weak transcription	Brain Angular Gyrus	brain
15	chr8:90975600-90995800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr8:90975800-90993200	Weak transcription	NHDF-Ad	bronchial
17	chr8:90976000-90993800	Weak transcription	Fetal Heart	heart
18	chr8:90976200-90993600	Weak transcription	Brain Hippocampus Middle	brain
19	chr8:90976200-90993800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:90976200-90993800	Weak transcription	Brain Germinal Matrix	brain
21	chr8:90976200-90995800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr8:90976400-90993600	Weak transcription	NHEK	skin
23	chr8:90976400-90993800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr8:90976400-90994400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr8:90976400-90995400	Weak transcription	Thymus	Thymus
26	chr8:90976400-90995600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr8:90976400-90995800	Weak transcription	Esophagus	oesophagus
28	chr8:90976600-90994400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr8:90976800-90993400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr8:90977000-90993400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr8:90977200-90993600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:90979600-90993000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr8:90980600-90993600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr8:90980800-90995600	Weak transcription	Ovary	ovary
35	chr8:90981000-90993000	Weak transcription	Brain Anterior Caudate	brain
36	chr8:90981600-90994800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr8:90982000-90994200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr8:90983200-90993600	Weak transcription	HepG2	liver
39	chr8:90983200-90993800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr8:90983200-90993800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr8:90983600-90994000	Weak transcription	NH-A	brain
42	chr8:90983800-90994800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr8:90983800-90995600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr8:90985400-90993200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr8:90986000-90993800	Weak transcription	HSMMtube	muscle
46	chr8:90986800-90993200	Strong transcription	HSMM	muscle
47	chr8:90987000-90994200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr8:90987000-90996000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr8:90987200-90993200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr8:90987200-90993800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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