Variant report

Variant	rs3002145
Chromosome Location	chr1:222807013-222807014
allele	A/C/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: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	chr1:222637935..222640112-chr1:222806335..222808096,3	MCF-7	breast:
2	chr1:222788507..222790055-chr1:222805799..222808069,2	K562	blood:
3	chr1:222637300..222641837-chr1:222805384..222811783,8	MCF-7	breast:
4	chr1:222797326..222799070-chr1:222805165..222807968,2	K562	blood:
5	chr1:222791343..222795260-chr1:222806268..222810918,6	K562	blood:
6	chr1:222806292..222810839-chr1:222815256..222818233,6	MCF-7	breast:
7	chr1:222803771..222808064-chr1:222812270..222818354,12	K562	blood:
8	chr1:222637338..222639462-chr1:222805621..222807759,2	K562	blood:
9	chr1:222762528..222765730-chr1:222806778..222808591,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225265	Chromatin interaction
ENSG00000234419	Chromatin interaction
ENSG00000154305	Chromatin interaction
ENSG00000229399	Chromatin interaction
ENSG00000143498	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17531007	1.00[CHB][hapmap]
rs17531580	1.00[CHB][hapmap]
rs17532757	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378605	1.00[ASW][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2936051	0.80[EUR][1000 genomes]
rs2936052	0.80[EUR][1000 genomes]
rs3008621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008622	0.80[EUR][1000 genomes]
rs3008630	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240934	1.00[ASW][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256814	1.00[ASN][1000 genomes]
rs61824333	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827168	0.80[EUR][1000 genomes]
rs904323	1.00[CHB][hapmap];1.00[ASN][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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription 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	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3002145	HOMER2	trans	parietal	SCAN
rs3002145	C1orf58	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222792400-222816600	Weak transcription	Small Intestine	intestine
2	chr1:222792600-222816600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:222792600-222817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:222793200-222816600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:222793200-222816600	Weak transcription	Hela-S3	cervix
6	chr1:222793600-222816600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:222794600-222807200	Strong transcription	Fetal Thymus	thymus
8	chr1:222794600-222809800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:222794600-222810400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:222794600-222810400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:222794600-222813400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:222794600-222813600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:222794600-222814000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:222794600-222815000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:222794800-222813200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:222794800-222813600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:222795200-222807600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:222795200-222807600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr1:222795200-222807800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:222795400-222807200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr1:222795400-222807600	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:222795400-222810400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:222795400-222810600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:222795400-222810600	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:222795400-222812000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:222795400-222813400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:222795600-222807200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr1:222795600-222807200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:222795600-222810600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:222795800-222810600	Strong transcription	Adipose Nuclei	Adipose
31	chr1:222796000-222807600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:222796200-222807800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:222797000-222809200	Strong transcription	Fetal Intestine Large	intestine
34	chr1:222797000-222812400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:222797400-222810600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:222797600-222810600	Strong transcription	Placenta	Placenta
37	chr1:222798200-222807600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:222798400-222807200	Strong transcription	Ovary	ovary
39	chr1:222798400-222812000	Strong transcription	Fetal Stomach	stomach
40	chr1:222798800-222808200	Strong transcription	Brain Hippocampus Middle	brain
41	chr1:222799000-222807200	Strong transcription	Fetal Brain Female	brain
42	chr1:222799000-222807600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:222799000-222807600	Strong transcription	Left Ventricle	heart
44	chr1:222799400-222807600	Strong transcription	Thymus	Thymus
45	chr1:222799600-222807600	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:222799600-222815000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:222800200-222807400	Strong transcription	Brain Cingulate Gyrus	brain
48	chr1:222800200-222809200	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr1:222800800-222808200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:222801000-222816600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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