Variant report

Variant	rs10889869
Chromosome Location	chr1:70877964-70877965
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70876526..70879847-chr1:71510519..71513789,3	K562	blood:
2	chr1:70688440..70690850-chr1:70877083..70879333,2	K562	blood:
3	chr1:70877206..70877981-chr10:52383708..52384377,2	Hela-S3	cervix:
4	chr1:70877825..70880614-chr1:70884736..70887414,2	K562	blood:
5	chr1:70819015..70821620-chr1:70875663..70878848,3	MCF-7	breast:
6	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:
7	chr1:70779446..70781152-chr1:70876074..70878497,2	MCF-7	breast:
8	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000050628	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000118454	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4650049	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs473334	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs577476	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs663649	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10889869	CTH	cis	lymphoblastoid	seeQTL
rs10889869	CTH	Cis_1M	lymphoblastoid	RTeQTL
rs10889869	LRRC40	cis	parietal	SCAN
rs10889869	LRRIQ3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70875600-70878000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:70875800-70878800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:70875800-70878800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr1:70875800-70879000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr1:70875800-70879000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:70875800-70879000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:70875800-70879800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:70875800-70880000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:70876000-70878000	Bivalent/Poised TSS	HepG2	liver
10	chr1:70876000-70878200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:70876000-70878200	Active TSS	Aorta	Aorta
14	chr1:70876000-70878200	Active TSS	Colonic Mucosa	Colon
15	chr1:70876000-70878200	Active TSS	Psoas Muscle	Psoas
16	chr1:70876000-70878200	Active TSS	GM12878-XiMat	blood
17	chr1:70876000-70878400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:70876000-70878400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:70876000-70878400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:70876000-70878400	Active TSS	Fetal Intestine Large	intestine
21	chr1:70876000-70878600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:70876000-70878600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:70876000-70878600	Active TSS	Ovary	ovary
24	chr1:70876000-70878600	Active TSS	Right Atrium	heart
25	chr1:70876000-70878600	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr1:70876000-70878800	Active TSS	H9 Cell Line	embryonic stem cell
27	chr1:70876000-70878800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:70876000-70878800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:70876000-70878800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:70876000-70878800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:70876000-70878800	Active TSS	Brain Substantia Nigra	brain
32	chr1:70876000-70878800	Active TSS	Right Ventricle	heart
33	chr1:70876000-70879000	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr1:70876000-70879000	Active TSS	K562	blood
35	chr1:70876200-70878000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:70876200-70878000	Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:70876200-70878000	Active TSS	Fetal Muscle Leg	muscle
38	chr1:70876200-70878000	Active TSS	Stomach Smooth Muscle	stomach
39	chr1:70876200-70878000	Active TSS	A549	lung
40	chr1:70876200-70878200	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr1:70876200-70878200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:70876200-70878200	Active TSS	Brain Angular Gyrus	brain
43	chr1:70876200-70878400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:70876200-70878400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr1:70876200-70878400	Active TSS	Pancreas	Pancrea
46	chr1:70876200-70878600	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr1:70876200-70878800	Active TSS	Fetal Brain Female	brain
48	chr1:70876200-70879000	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr1:70876200-70879600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:70876400-70878200	Active TSS	NHEK	skin

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