Variant report

Variant	rs1218565
Chromosome Location	chr1:154817687-154817688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154807688..154810280-chr1:154815696..154818405,2	K562	blood:
2	chr1:154812878..154815262-chr1:154817032..154818549,2	K562	blood:
3	chr1:154793548..154796604-chr1:154817553..154820667,3	MCF-7	breast:

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1218567	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1218568	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426985	0.81[AMR][1000 genomes]
rs883905	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1218565	HAPLN2	cis	parietal	SCAN
rs1218565	CTSS	cis	parietal	SCAN
rs1218565	CLK2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154803200-154824600	Enhancers	Fetal Brain Male	brain
2	chr1:154806200-154818000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:154806800-154817800	Weak transcription	Right Ventricle	heart
4	chr1:154808400-154823600	Enhancers	Fetal Muscle Leg	muscle
5	chr1:154810400-154817800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:154812000-154818600	Enhancers	Fetal Stomach	stomach
7	chr1:154812000-154822000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:154812400-154824400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:154812600-154822000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:154813000-154818600	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:154813200-154818400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:154813200-154818600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:154813200-154818600	Weak transcription	Fetal Kidney	kidney
14	chr1:154813400-154817800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:154813400-154818000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:154813400-154818000	Weak transcription	Right Atrium	heart
17	chr1:154813600-154817800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:154813600-154818000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:154813600-154818000	Weak transcription	Spleen	Spleen
20	chr1:154813600-154818400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:154813600-154818400	Weak transcription	Lung	lung
22	chr1:154813800-154821600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:154813800-154822600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:154814000-154818600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:154814800-154820400	Weak transcription	Pancreas	Pancrea
26	chr1:154815800-154820200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:154815800-154823200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr1:154816600-154818000	Weak transcription	Left Ventricle	heart
29	chr1:154816800-154817800	Weak transcription	Fetal Intestine Large	intestine
30	chr1:154816800-154818000	Weak transcription	Brain Substantia Nigra	brain
31	chr1:154816800-154818400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:154816800-154819000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:154816800-154819200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:154816800-154820200	Enhancers	Fetal Brain Female	brain
35	chr1:154817000-154818000	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:154817000-154818000	Weak transcription	Fetal Lung	lung
37	chr1:154817000-154818400	Enhancers	GM12878-XiMat	blood
38	chr1:154817000-154818600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:154817000-154818800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:154817000-154819200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:154817000-154820200	Enhancers	Brain Germinal Matrix	brain
42	chr1:154817600-154818400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr1:154817600-154819000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:154817600-154819400	Enhancers	Fetal Intestine Small	intestine
45	chr1:154817600-154819400	Enhancers	Fetal Thymus	thymus
46	chr1:154817600-154820200	Enhancers	Brain Anterior Caudate	brain
47	chr1:154817600-154820200	Enhancers	Brain Cingulate Gyrus	brain
48	chr1:154817600-154821200	Enhancers	Psoas Muscle	Psoas

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