Variant report

Variant	rs2996294
Chromosome Location	chr1:113416122-113416123
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113257969..113259766-chr1:113414429..113416544,2	K562	blood:
2	chr1:113413685..113416683-chr1:113491542..113494143,2	K562	blood:
3	chr1:113415161..113418488-chr1:113420570..113424322,4	K562	blood:
4	chr1:113414731..113417256-chr1:113497022..113499484,2	K562	blood:
5	chr1:113415018..113417156-chr1:113420570..113423546,3	K562	blood:
6	chr1:113255585..113257098-chr1:113416016..113418840,2	K562	blood:

Variant related genes	Relation type
ENSG00000155367	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000226419	Chromatin interaction
ENSG00000155380	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11576349	0.81[EUR][1000 genomes]
rs12068893	0.81[EUR][1000 genomes]
rs1216537	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1235629	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1237670	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2360008	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2996389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2996391	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2996392	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429495	0.81[EUR][1000 genomes]
rs9429496	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv818378	chr1:113263711-113434818	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1008434	chr1:113288282-113447426	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
12	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
13	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
14	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
15	esv3362439	chr1:113376621-113450321	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2996294	LRIG2	cis	cerebellum	SCAN
rs2996294	ATP1A1	cis	cerebellum	SCAN
rs2996294	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL
rs2996294	DDX20	cis	cerebellum	SCAN
rs2996294	OVGP1	cis	cerebellum	SCAN
rs2996294	DENND2C	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113405800-113418200	Enhancers	Placenta	Placenta
2	chr1:113412200-113420200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:113412200-113420200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:113412400-113416800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:113412400-113416800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:113412400-113416800	Weak transcription	HMEC	breast
7	chr1:113412400-113416800	Weak transcription	NHEK	skin
8	chr1:113413400-113416600	Enhancers	Fetal Intestine Large	intestine
9	chr1:113413400-113417600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr1:113414600-113416600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:113415000-113424600	Weak transcription	Right Atrium	heart
12	chr1:113415200-113416200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:113415200-113417000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:113415200-113417200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:113415400-113416600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:113415400-113416800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:113415600-113416200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:113415600-113421000	Weak transcription	Colonic Mucosa	Colon
19	chr1:113415600-113423400	Weak transcription	Osteobl	bone
20	chr1:113415800-113416800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:113415800-113416800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:113415800-113416800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:113415800-113420400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:113415800-113420400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:113415800-113420800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:113415800-113421000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:113415800-113422000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:113415800-113423200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:113416000-113416200	Enhancers	K562	blood
30	chr1:113416000-113416800	Weak transcription	Fetal Intestine Small	intestine
31	chr1:113416000-113420200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:113416000-113420200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:113416000-113420200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:113416000-113420200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:113416000-113420400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:113416000-113420600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:113416000-113423200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:113416000-113424600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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