Variant report

Variant	rs3796541
Chromosome Location	chr4:57270835-57270836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57256994..57259922-chr4:57269239..57271312,2	K562	blood:
2	chr4:57269980..57272538-chr4:57276339..57278488,2	K562	blood:
3	chr4:57261443..57262969-chr4:57269868..57272239,2	K562	blood:
4	chr4:57268824..57271246-chr4:57301014..57303212,2	K562	blood:

Variant related genes	Relation type
ENSG00000268171	Chromatin interaction
ENSG00000270147	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10434445	0.84[EUR][1000 genomes]
rs1060472	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11133442	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12501334	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12501502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12503412	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12504291	0.81[AMR][1000 genomes]
rs12510712	0.81[EUR][1000 genomes]
rs12511770	0.81[AMR][1000 genomes]
rs1474179	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1520026	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1520030	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1967559	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2271923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28866881	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4346704	0.80[AMR][1000 genomes]
rs4493603	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864583	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5010012	0.89[EUR][1000 genomes]
rs56392224	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58151706	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66810706	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6820314	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6821301	0.81[AMR][1000 genomes]
rs6829250	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6832797	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6834696	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6846895	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6855041	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664841	0.81[AMR][1000 genomes]

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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3796541	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
3	chr4:57254600-57271600	Weak transcription	Ovary	ovary
4	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
5	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:57254800-57271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:57254800-57273200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
12	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
13	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:57255000-57271400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:57255200-57271600	Weak transcription	NHEK	skin
16	chr4:57255200-57272200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:57255200-57275600	Weak transcription	NHLF	lung
18	chr4:57255200-57276400	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:57255200-57276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:57255200-57276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:57255200-57276600	Weak transcription	Brain Substantia Nigra	brain
22	chr4:57255400-57272400	Weak transcription	Fetal Brain Male	brain
23	chr4:57255400-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:57255600-57272000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:57255600-57275600	Weak transcription	Fetal Brain Female	brain
26	chr4:57255800-57271600	Weak transcription	Hela-S3	cervix
27	chr4:57255800-57276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:57256000-57272200	Weak transcription	Adipose Nuclei	Adipose
29	chr4:57256000-57274200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:57256000-57276400	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:57256200-57276600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:57256400-57276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:57257600-57272600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:57257600-57274200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:57258400-57274200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:57258800-57271800	Weak transcription	Brain Angular Gyrus	brain
37	chr4:57259000-57274000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:57259400-57275600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:57260200-57274200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:57260600-57273000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:57260800-57274200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:57261000-57273200	Strong transcription	Dnd41	blood
43	chr4:57261200-57271600	Weak transcription	Aorta	Aorta
44	chr4:57261200-57273000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:57262000-57273400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:57263400-57271600	Weak transcription	HSMMtube	muscle
47	chr4:57264000-57274000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:57264200-57274000	Strong transcription	GM12878-XiMat	blood
49	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
50	chr4:57264400-57276400	Weak transcription	Brain Inferior Temporal Lobe	brain

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