Variant report

Variant	rs1338285
Chromosome Location	chr1:210475254-210475255
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210472726..210476795-chr1:210544838..210548404,4	MCF-7	breast:
2	chr1:210472681..210476140-chr1:210544335..210548471,5	K562	blood:
3	chr1:210465950..210468476-chr1:210473987..210476235,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1040563	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12739013	0.80[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes]
rs12739023	0.84[EUR][1000 genomes]
rs655829	0.83[EUR][1000 genomes]
rs655847	0.83[EUR][1000 genomes]
rs656753	0.80[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs6658075	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs670441	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1338285	HHAT	cis	parietal	SCAN
rs1338285	CAMK1G	cis	cerebellum	SCAN
rs1338285	SERTAD4	cis	parietal	SCAN
rs1338285	SYT14	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210466800-210477400	Enhancers	Fetal Muscle Leg	muscle
2	chr1:210472400-210475400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:210472400-210477000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:210473600-210475600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:210473800-210475800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:210474000-210475600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:210474000-210476400	Enhancers	Adipose Nuclei	Adipose
8	chr1:210474000-210476400	Enhancers	Fetal Heart	heart
9	chr1:210474200-210475400	Enhancers	Brain Substantia Nigra	brain
10	chr1:210474200-210475600	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:210474200-210475600	Enhancers	Stomach Mucosa	stomach
12	chr1:210474200-210475800	Enhancers	NHDF-Ad	bronchial
13	chr1:210474200-210476000	Enhancers	HSMMtube	muscle
14	chr1:210474200-210476200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:210474200-210476200	Enhancers	Psoas Muscle	Psoas
16	chr1:210474200-210476400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:210474200-210477600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:210474400-210475400	Bivalent Enhancer	Fetal Brain Male	brain
19	chr1:210474400-210476000	Enhancers	Brain Anterior Caudate	brain
20	chr1:210474400-210476000	Enhancers	Brain Germinal Matrix	brain
21	chr1:210474600-210476000	Enhancers	Fetal Stomach	stomach
22	chr1:210474800-210475400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:210474800-210475400	Bivalent Enhancer	NHLF	lung
24	chr1:210474800-210475600	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr1:210474800-210475600	Enhancers	HSMM	muscle
26	chr1:210474800-210475800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:210474800-210476000	Enhancers	Fetal Brain Female	brain
28	chr1:210475000-210475400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:210475000-210475400	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr1:210475000-210475400	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr1:210475000-210475400	Enhancers	Ovary	ovary
32	chr1:210475000-210476000	Enhancers	Rectal Smooth Muscle	rectum
33	chr1:210475000-210476200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr1:210475200-210475800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr1:210475200-210477000	Enhancers	Esophagus	oesophagus

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