Variant report

Variant	rs2298294
Chromosome Location	chr1:151701345-151701346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151688007..151690432-chr1:151699562..151701503,2	MCF-7	breast:
2	chr1:151693523..151696845-chr1:151699758..151701957,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL589765.1-1	chr1:151701242-151701369	NONHSAT006413
2	lnc-AL589765.1-1	chr1:151701242-151701369	NONHSAT006412
3	lnc-AL589765.1-1	chr1:151701242-151701369	NONHSAT006414

Variant related genes	Relation type
ENSG00000159409	Chromatin interaction
ENSG00000178796	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11204878	0.88[EUR][1000 genomes]
rs12402668	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2275920	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2275921	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280475	0.81[CHB][hapmap]
rs57696433	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59527020	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61501378	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2298294	LCE1C	cis	parietal	SCAN
rs2298294	BCL9	cis	cerebellum	SCAN
rs2298294	SPRR2G	cis	cerebellum	SCAN
rs2298294	LINGO4	cis	cerebellum	SCAN
rs2298294	MTMR11	cis	cerebellum	SCAN
rs2298294	SLC27A3	cis	cerebellum	SCAN
rs2298294	SPRR2B	cis	cerebellum	SCAN
rs2298294	GATAD2B	cis	cerebellum	SCAN
rs2298294	TDRKH	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151699200-151703800	Enhancers	Fetal Brain Male	brain
2	chr1:151699400-151702400	Weak transcription	Colonic Mucosa	Colon
3	chr1:151700000-151701600	Weak transcription	Fetal Intestine Large	intestine
4	chr1:151700000-151702000	Enhancers	Fetal Stomach	stomach
5	chr1:151700200-151701800	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr1:151700400-151701600	Enhancers	Fetal Heart	heart
7	chr1:151700400-151701800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:151700400-151702800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:151700400-151703000	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr1:151700600-151701400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:151700600-151701400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:151700600-151701400	Active TSS	Brain Cingulate Gyrus	brain
13	chr1:151700600-151701400	Active TSS	Brain Substantia Nigra	brain
14	chr1:151700600-151701400	Active TSS	Fetal Brain Female	brain
15	chr1:151700600-151701400	Enhancers	Psoas Muscle	Psoas
16	chr1:151700600-151701400	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:151700600-151701600	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr1:151700600-151701600	Bivalent Enhancer	HepG2	liver
19	chr1:151700600-151701800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:151700600-151701800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:151700600-151702000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:151700600-151702600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:151700800-151701400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
24	chr1:151700800-151701400	Active TSS	Colon Smooth Muscle	Colon
25	chr1:151700800-151701400	Weak transcription	Fetal Intestine Small	intestine
26	chr1:151700800-151701800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:151700800-151701800	Active TSS	Stomach Smooth Muscle	stomach
28	chr1:151700800-151702000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:151700800-151702400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:151700800-151704000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:151700800-151709800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:151701000-151701400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr1:151701000-151701400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr1:151701000-151701400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:151701000-151701600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:151701000-151701800	Enhancers	HSMM	muscle
37	chr1:151701000-151702000	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr1:151701000-151702000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:151701000-151702400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:151701200-151701400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
41	chr1:151701200-151701400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr1:151701200-151701400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:151701200-151701400	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr1:151701200-151701400	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr1:151701200-151701400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:151701200-151701400	Flanking Active TSS	HSMMtube	muscle
47	chr1:151701200-151701600	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr1:151701200-151701800	Enhancers	Brain Hippocampus Middle	brain
49	chr1:151701200-151702000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr1:151701200-151702000	Weak transcription	Right Atrium	heart

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