Variant report

Variant	rs16856475
Chromosome Location	chr1:180850720-180850721
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	chr1:180846972..180853051-chr1:181055773..181063614,10	MCF-7	breast:
2	chr1:180850662..180852317-chr1:180933020..180935917,2	K562	blood:
3	chr1:180501736..180504580-chr1:180849617..180851202,2	K562	blood:
4	chr1:180849796..180851972-chr1:181110307..181113193,2	MCF-7	breast:
5	chr1:180848547..180852061-chr1:181053599..181056742,3	MCF-7	breast:
6	chr1:180850269..180851818-chr1:181135334..181136683,10	MCF-7	breast:
7	chr1:180849811..180851965-chr1:181072778..181074539,2	MCF-7	breast:
8	chr1:180849682..180853088-chr1:181056991..181059628,4	K562	blood:
9	chr1:180849863..180851365-chr1:180863238..180865700,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000251520	Chromatin interaction
ENSG00000162783	Chromatin interaction
ENSG00000272198	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10914126	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11484676	1.00[ASN][1000 genomes]
rs11807408	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11807424	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11808588	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809124	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810413	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11811353	1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12075005	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12749805	1.00[ASN][1000 genomes]
rs16856374	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16856405	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16856438	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16856482	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17301454	1.00[ASN][1000 genomes]
rs34815509	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789370	1.00[JPT][hapmap]
rs41268446	1.00[ASN][1000 genomes]
rs4652536	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652537	1.00[JPT][hapmap]
rs58427257	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58685814	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58837546	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61809318	1.00[ASN][1000 genomes]
rs61809333	1.00[ASN][1000 genomes]
rs6692550	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7556184	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs950830	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180773800-180853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:180779800-180850800	Weak transcription	Small Intestine	intestine
3	chr1:180796400-180851000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:180805800-180881000	Weak transcription	Aorta	Aorta
5	chr1:180812200-180867000	Weak transcription	Ovary	ovary
6	chr1:180819200-180851000	Weak transcription	Fetal Brain Male	brain
7	chr1:180822000-180862800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:180822800-180862800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:180823000-180854600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:180823600-180860000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:180823800-180851000	Weak transcription	Fetal Kidney	kidney
12	chr1:180823800-180851400	Weak transcription	Pancreas	Pancrea
13	chr1:180823800-180862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:180824000-180867600	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:180824000-180880800	Weak transcription	Right Ventricle	heart
16	chr1:180824200-180851000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:180827800-180856600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:180828000-180852400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:180828000-180853200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:180828000-180853200	Weak transcription	NHEK	skin
21	chr1:180828600-180867800	Weak transcription	HSMM	muscle
22	chr1:180828800-180851000	Weak transcription	Brain Germinal Matrix	brain
23	chr1:180830000-180867600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:180831000-180851400	Weak transcription	Fetal Thymus	thymus
25	chr1:180831200-180858600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:180831600-180851000	Weak transcription	Brain Angular Gyrus	brain
27	chr1:180831600-180852600	Weak transcription	Fetal Lung	lung
28	chr1:180832400-180850800	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:180832400-180850800	Weak transcription	NH-A	brain
30	chr1:180832400-180851000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:180832400-180851000	Weak transcription	Brain Anterior Caudate	brain
32	chr1:180832400-180853200	Weak transcription	Fetal Stomach	stomach
33	chr1:180832600-180854400	Weak transcription	Liver	Liver
34	chr1:180832800-180861800	Weak transcription	HepG2	liver
35	chr1:180833200-180851000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:180834200-180851000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:180834800-180855800	Weak transcription	Gastric	stomach
38	chr1:180835400-180862800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:180835600-180855400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:180835800-180856600	Weak transcription	Fetal Intestine Large	intestine
41	chr1:180835800-180858800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:180835800-180861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:180835800-180870400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:180839400-180851000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:180840800-180851000	Weak transcription	HSMMtube	muscle
46	chr1:180841000-180850800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:180841000-180867800	Weak transcription	Lung	lung
48	chr1:180841800-180851200	Weak transcription	Thymus	Thymus
49	chr1:180841800-180855000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:180841800-180856000	Weak transcription	Fetal Muscle Trunk	muscle

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