Variant report

Variant	rs2151540
Chromosome Location	chr1:70908457-70908458
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:70905812-70910297	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70898237..70900336-chr1:70907691..70909600,2	K562	blood:

Variant related genes	Relation type
ENSG00000271992	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17131261	0.82[YRI][hapmap]
rs57217591	0.81[AFR][1000 genomes]
rs58518248	0.94[AFR][1000 genomes]
rs59320305	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv461828	chr1:70880717-70922360	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv546456	chr1:70880717-70922360	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2151540	HHLA3	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70878200-70909600	Weak transcription	Gastric	stomach
2	chr1:70884400-70909000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:70895800-70912000	Weak transcription	Hela-S3	cervix
4	chr1:70897000-70909600	Weak transcription	Pancreas	Pancrea
5	chr1:70898200-70908600	Strong transcription	Liver	Liver
6	chr1:70900200-70913800	Weak transcription	Dnd41	blood
7	chr1:70900200-70914800	Weak transcription	K562	blood
8	chr1:70902000-70909600	Weak transcription	Lung	lung
9	chr1:70904000-70908800	Weak transcription	HepG2	liver
10	chr1:70904600-70915000	Weak transcription	Aorta	Aorta
11	chr1:70905000-70909600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:70905000-70910000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:70905400-70909400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:70906400-70910400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:70906600-70910000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr1:70906600-70910000	Weak transcription	Ovary	ovary
17	chr1:70906800-70909200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:70906800-70910200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:70907000-70909200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:70907000-70910200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:70907000-70914000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:70907200-70909200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:70907200-70910200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:70907400-70908800	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr1:70907400-70910200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:70907600-70908600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:70907600-70908800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:70907600-70909400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:70907800-70908800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:70908000-70908600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr1:70908000-70908600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr1:70908000-70908600	Enhancers	NHDF-Ad	bronchial
33	chr1:70908000-70909400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr1:70908200-70910000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:70908400-70908600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:70908400-70909400	Weak transcription	Brain Germinal Matrix	brain
37	chr1:70908400-70910000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:70908400-70912800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:70908400-70915000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:70908400-70918600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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