Variant report

Variant	rs16858529
Chromosome Location	chr1:161697149-161697150
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161695790..161697784-chr8:91655626..91657821,2	MCF-7	breast:
2	chr1:161696233..161698594-chr1:161718488..161721013,2	MCF-7	breast:
3	chr1:161696482..161699035-chr1:161718061..161722028,6	K562	blood:
4	chr1:161657417..161659539-chr1:161696325..161698709,3	K562	blood:
5	chr1:161474965..161476524-chr1:161694397..161697249,2	K562	blood:
6	chr1:161648385..161650314-chr1:161696093..161698220,2	K562	blood:
7	chr1:161696672..161698764-chr1:161719597..161721628,3	K562	blood:
8	chr1:161654373..161658306-chr1:161696464..161699587,3	MCF-7	breast:
9	chr1:161694367..161698874-chr1:161718174..161721030,6	MCF-7	breast:
10	chr1:161696651..161697360-chr16:2961887..2962457,2	NB4	blood:
11	chr1:161651291..161653505-chr1:161696476..161699114,3	K562	blood:
12	chr1:161695918..161698329-chr1:161735226..161737077,2	MCF-7	breast:
13	chr1:161683127..161685809-chr1:161696033..161698160,3	MCF-7	breast:
14	chr1:161535342..161537175-chr1:161695826..161698506,2	MCF-7	breast:
15	chr1:161696512..161697495-chr11:66610830..66611790,2	NB4	blood:
16	chr1:161696821..161698460-chr1:161718041..161719561,2	K562	blood:
17	chr1:161640986..161643411-chr1:161696404..161699095,2	MCF-7	breast:
18	chr1:161696699..161697640-chr1:161719530..161720155,2	MCF-7	breast:
19	chr1:161645664..161648632-chr1:161696817..161700044,3	K562	blood:
20	chr1:161474965..161477021-chr1:161694558..161697249,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143226	Chromatin interaction
ENSG00000059122	Chromatin interaction
ENSG00000081721	Chromatin interaction
ENSG00000226889	Chromatin interaction
ENSG00000213075	Chromatin interaction
ENSG00000180694	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000173653	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10494356	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10799934	0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10917746	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10917753	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10917754	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10917809	0.91[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11586479	0.84[ASN][1000 genomes]
rs12048671	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12567036	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16858733	0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs1954174	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[ASN][1000 genomes]
rs2050887	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4468140	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56270452	0.89[EUR][1000 genomes]
rs6427619	0.81[CHB][hapmap]
rs6427620	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6697814	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67476681	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72704099	0.91[ASN][1000 genomes]
rs7522783	0.84[ASN][1000 genomes]
rs7525788	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs7549830	0.82[CHD][hapmap]
rs7549967	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs905592	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv516773	chr1:161691433-161702763	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
6	nsv464195	chr1:161693003-161702792	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
7	nsv548076	chr1:161693003-161702792	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
8	esv3343743	chr1:161695553-161698101	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161695400-161697200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:161695400-161697400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
3	chr1:161695400-161697600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:161695400-161697600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:161695400-161697600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:161695400-161697600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:161695400-161697600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr1:161695400-161697600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:161695400-161697600	Active TSS	Brain Substantia Nigra	brain
10	chr1:161695400-161697600	Active TSS	Fetal Kidney	kidney
11	chr1:161695400-161697800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr1:161695400-161697800	Active TSS	Brain Angular Gyrus	brain
13	chr1:161695400-161697800	Active TSS	Ovary	ovary
14	chr1:161695400-161698000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr1:161695400-161698200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:161695600-161697200	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr1:161695600-161697200	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr1:161695600-161697200	Active TSS	Osteobl	bone
19	chr1:161695600-161697400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
20	chr1:161695600-161697600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:161695600-161697600	Active TSS	Aorta	Aorta
22	chr1:161695600-161697600	Active TSS	Brain Hippocampus Middle	brain
23	chr1:161695600-161697600	Active TSS	Colon Smooth Muscle	Colon
24	chr1:161695600-161697600	Active TSS	Psoas Muscle	Psoas
25	chr1:161695600-161697600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
26	chr1:161695600-161697800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:161695600-161697800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr1:161695600-161697800	Active TSS	Brain Anterior Caudate	brain
29	chr1:161695800-161697200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:161695800-161697200	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr1:161695800-161697200	Active TSS	HSMMtube	muscle
32	chr1:161695800-161697400	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr1:161695800-161697400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:161695800-161697400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:161695800-161697400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
36	chr1:161695800-161697400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:161695800-161697400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
38	chr1:161695800-161697400	Active TSS	Left Ventricle	heart
39	chr1:161695800-161697400	Active TSS	Right Ventricle	heart
40	chr1:161695800-161697400	Active TSS	Small Intestine	intestine
41	chr1:161695800-161697400	Active TSS	GM12878-XiMat	blood
42	chr1:161695800-161697600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:161695800-161697600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:161695800-161697600	Active TSS	Brain Cingulate Gyrus	brain
45	chr1:161695800-161697600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr1:161695800-161697600	Active TSS	Gastric	stomach
47	chr1:161695800-161697600	Active TSS	Lung	lung
48	chr1:161695800-161697600	Active TSS	A549	lung
49	chr1:161695800-161697800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:161695800-161697800	Active TSS	NHDF-Ad	bronchial

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