Variant report

Variant	rs35138279
Chromosome Location	chr1:153944594-153944595
allele	C/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	chr1:153944575-153946711	GM12891	blood:	n/a	n/a
2	MTA3	chr1:153944558-153946114	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:153944530-153946631	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:153944437-153946874	GM12892	blood:	n/a	n/a
5	POU2F2	chr1:153944594-153945066	GM12891	blood:	n/a	chr1:153944871-153944882
6	POLR2A	chr1:153944581-153944877	K562	blood:	n/a	n/a
7	POLR2A	chr1:153944483-153946780	GM12891	blood:	n/a	n/a
8	POLR2A	chr1:153944538-153946731	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:153944561-153944891	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:153944532-153947599	K562	blood:	n/a	n/a
11	POLR2A	chr1:153944484-153945199	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:153944553-153946803	K562	blood:	n/a	n/a
13	POLR2A	chr1:153944578-153945918	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:153944572-153947316	GM12891	blood:	n/a	n/a
15	POLR2A	chr1:153944198-153946956	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:153944497-153946763	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:153944477-153946806	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:153944547-153946669	HL-60	blood:	n/a	n/a
19	POLR2A	chr1:153944567-153946779	GM12892	blood:	n/a	n/a
20	POLR2A	chr1:153944451-153946873	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr1:153944350-153947570	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr1:153944513-153945434	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153895740..153897837-chr1:153943889..153946468,2	K562	blood:
2	chr1:153915931..153921352-chr1:153944041..153951714,10	K562	blood:

Variant related genes	Relation type
SLC39A1	TF binding region
ENSG00000198837	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11265027	1.00[CHD][hapmap]
rs12563892	1.00[CHD][hapmap]
rs12755932	1.00[CHD][hapmap]
rs16835602	1.00[CHD][hapmap]
rs34612917	1.00[CHD][hapmap]
rs36106412	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35138279	SEMA4A	cis	parietal	SCAN
rs35138279	ADAM15	cis	parietal	SCAN
rs35138279	GATAD2B	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153940800-153945600	Weak transcription	Primary T cells from cord blood	blood
2	chr1:153940800-153946200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:153940800-153947000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:153941000-153946000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:153941000-153946200	Weak transcription	Small Intestine	intestine
6	chr1:153941200-153944800	Weak transcription	Brain Anterior Caudate	brain
7	chr1:153941200-153944800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:153941200-153944800	Weak transcription	HSMM	muscle
9	chr1:153941200-153945000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:153941200-153945000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:153941200-153945400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:153941200-153945400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:153941200-153945400	Weak transcription	Brain Substantia Nigra	brain
14	chr1:153941200-153945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:153941200-153945600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:153941200-153945600	Weak transcription	Aorta	Aorta
17	chr1:153941200-153945600	Weak transcription	Brain Angular Gyrus	brain
18	chr1:153941200-153945600	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:153941200-153945600	Weak transcription	Esophagus	oesophagus
20	chr1:153941200-153945600	Weak transcription	Left Ventricle	heart
21	chr1:153941200-153945800	Weak transcription	Ovary	ovary
22	chr1:153941200-153945800	Weak transcription	A549	lung
23	chr1:153941200-153945800	Weak transcription	HSMMtube	muscle
24	chr1:153941200-153946000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:153941200-153946200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:153941200-153946200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:153941200-153946200	Weak transcription	Colonic Mucosa	Colon
28	chr1:153941200-153946400	Weak transcription	NHDF-Ad	bronchial
29	chr1:153941200-153948200	Weak transcription	Stomach Mucosa	stomach
30	chr1:153941200-153948600	Weak transcription	Psoas Muscle	Psoas
31	chr1:153941200-153949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:153941400-153944600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:153941400-153944600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:153941400-153944600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:153941400-153944600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:153941400-153944800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:153941400-153945000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:153941400-153945000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:153941400-153945000	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:153941400-153945200	Weak transcription	NHLF	lung
41	chr1:153941400-153945400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:153941400-153945400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:153941400-153945400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:153941400-153945400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:153941400-153945400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:153941400-153945800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:153941400-153945800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:153941400-153945800	Weak transcription	Osteobl	bone
49	chr1:153941400-153946000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:153941400-153946000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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