Variant report

Variant	rs1338912
Chromosome Location	chr1:239702000-239702001
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10159107	1.00[EUR][1000 genomes]
rs10159110	1.00[EUR][1000 genomes]
rs10159111	1.00[EUR][1000 genomes]
rs12240106	0.85[AMR][1000 genomes]
rs1338911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1338913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16838397	0.85[AMR][1000 genomes]
rs16838400	0.85[AMR][1000 genomes]
rs16838446	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16838467	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16838472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16838502	0.85[AMR][1000 genomes]
rs1938229	1.00[MEX][hapmap]
rs56286075	1.00[EUR][1000 genomes]
rs59092744	1.00[EUR][1000 genomes]
rs6671073	1.00[EUR][1000 genomes]
rs6677208	1.00[EUR][1000 genomes]
rs6699693	1.00[EUR][1000 genomes]
rs73114786	1.00[EUR][1000 genomes]
rs73114796	1.00[EUR][1000 genomes]
rs73116726	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73116729	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73116739	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73116743	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73120617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73122644	1.00[EUR][1000 genomes]
rs74149063	1.00[EUR][1000 genomes]
rs74149065	1.00[EUR][1000 genomes]
rs74149066	1.00[EUR][1000 genomes]
rs74149069	1.00[EUR][1000 genomes]
rs74149070	1.00[EUR][1000 genomes]
rs9970217	1.00[EUR][1000 genomes]
rs9970229	1.00[EUR][1000 genomes]
rs9970997	1.00[EUR][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	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1338912	SH2B2	trans	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239699200-239702400	Enhancers	Stomach Smooth Muscle	stomach
2	chr1:239699200-239702600	Enhancers	Rectal Smooth Muscle	rectum
3	chr1:239699400-239702600	Weak transcription	Pancreas	Pancrea
4	chr1:239699400-239703200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:239699600-239703600	Enhancers	Colon Smooth Muscle	Colon
6	chr1:239700000-239702200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:239700000-239703000	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr1:239700200-239702600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:239700400-239702800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:239700400-239704000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:239700600-239702000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:239700600-239702600	Enhancers	Fetal Stomach	stomach
13	chr1:239700600-239702800	Enhancers	Ovary	ovary
14	chr1:239700600-239703400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:239700800-239703800	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:239701000-239702600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:239701200-239702000	Enhancers	Adipose Nuclei	Adipose
18	chr1:239701200-239702200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:239701200-239702600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:239701200-239702600	Enhancers	Fetal Brain Male	brain
21	chr1:239701200-239703000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:239701400-239702200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:239701400-239702600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr1:239701400-239702600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr1:239701400-239711800	Weak transcription	Fetal Intestine Small	intestine
26	chr1:239701600-239702000	Enhancers	Fetal Kidney	kidney
27	chr1:239701800-239702400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr1:239701800-239702600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:239702000-239703000	Weak transcription	Adipose Nuclei	Adipose
30	chr1:239702000-239711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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