Variant report

Variant	rs3738199
Chromosome Location	chr1:211545344-211545345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:211545301..211548171-chr1:211550242..211553201,2	K562	blood:
2	chr1:211544391..211549113-chr1:211554192..211558481,8	K562	blood:
3	chr1:211542319..211548394-chr1:211548704..211553201,8	K562	blood:
4	chr1:211531701..211533938-chr1:211544788..211546541,2	K562	blood:

Variant related genes	Relation type
ENSG00000153363	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1055565	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1084981	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10863888	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11580084	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs11811405	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap]
rs12027724	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs12116749	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs12118279	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap]
rs1533217	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs1663522	0.96[CEU][hapmap];0.80[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2063569	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2798559	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2920911	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3002258	0.81[EUR][1000 genomes]
rs3111257	0.85[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap]
rs3111258	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap]
rs3767377	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs3767378	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs4406705	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs4951520	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[TSI][hapmap]
rs4951523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951741	0.80[EUR][1000 genomes]
rs4951742	0.80[EUR][1000 genomes]
rs6689078	0.81[CHB][hapmap]
rs6700747	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap]
rs6703361	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7520989	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs7550702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs784369	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs784379	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs784382	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs784383	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs784385	0.91[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs784389	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762141	chr1:211538685-211603843	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3738199	C1orf74	cis	parietal	SCAN
rs3738199	LAMB3	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211510600-211555400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:211514800-211552200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:211515000-211555000	Weak transcription	Hela-S3	cervix
4	chr1:211515000-211555800	Weak transcription	Esophagus	oesophagus
5	chr1:211515400-211548400	Weak transcription	Stomach Mucosa	stomach
6	chr1:211519400-211549000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:211519800-211547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:211519800-211548600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:211521200-211550200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:211521600-211555200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:211525000-211555600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:211525400-211550200	Weak transcription	NHDF-Ad	bronchial
13	chr1:211525400-211555000	Weak transcription	Fetal Lung	lung
14	chr1:211525600-211548200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:211525600-211550200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:211526400-211546400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:211526600-211555400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:211526800-211550800	Weak transcription	Small Intestine	intestine
19	chr1:211527400-211550400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:211528000-211551400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:211528200-211550600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:211528400-211547600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:211528800-211554600	Weak transcription	Psoas Muscle	Psoas
24	chr1:211529400-211550400	Strong transcription	Fetal Thymus	thymus
25	chr1:211529600-211551200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:211530200-211555800	Weak transcription	Pancreas	Pancrea
27	chr1:211530400-211545600	Weak transcription	Lung	lung
28	chr1:211530400-211555200	Weak transcription	Brain Anterior Caudate	brain
29	chr1:211530600-211548800	Weak transcription	Fetal Intestine Small	intestine
30	chr1:211530600-211550000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:211530600-211555600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:211530800-211545400	Weak transcription	Fetal Intestine Large	intestine
33	chr1:211531000-211551600	Weak transcription	NHLF	lung
34	chr1:211531200-211550000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:211531200-211550000	Weak transcription	HSMM	muscle
36	chr1:211533400-211547200	Weak transcription	Spleen	Spleen
37	chr1:211533400-211550200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:211533400-211551200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:211533400-211552000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:211533800-211554800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:211534600-211545400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:211534600-211546200	Weak transcription	Placenta	Placenta
43	chr1:211534600-211547400	Weak transcription	HSMMtube	muscle
44	chr1:211534600-211555800	Weak transcription	Gastric	stomach
45	chr1:211535000-211549800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:211535000-211555000	Weak transcription	A549	lung
47	chr1:211535400-211555800	Weak transcription	Left Ventricle	heart
48	chr1:211537200-211551200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:211538000-211546800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:211538200-211546200	Strong transcription	Stomach Smooth Muscle	stomach

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