Variant report

Variant	rs4970940
Chromosome Location	chr1:151046642-151046643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151000849..151004136-chr1:151043439..151047441,3	K562	blood:
2	chr1:151042783..151045327-chr1:151046112..151049113,3	K562	blood:

Variant related genes	Relation type
ENSG00000143458	Chromatin interaction
ENSG00000197622	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10749659	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204771	0.80[EUR][1000 genomes]
rs11204779	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12049116	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12093562	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12134957	0.90[ASN][1000 genomes]
rs15740	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4970936	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4970939	0.80[AMR][1000 genomes]
rs4970941	0.81[ASN][1000 genomes]
rs6587552	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6697617	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6704195	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7514185	0.87[AFR][1000 genomes]
rs7522608	0.86[ASN][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4970940	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL
rs4970940	BNIPL	cis	Thyroid	GTEx
rs4970940	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs4970940	BNIPL	cis	lung	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151043600-151048200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:151043600-151048800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:151043600-151049600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:151043600-151050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:151043800-151047200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:151043800-151056200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:151044000-151047000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:151044000-151047400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:151044000-151048800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:151044000-151062800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:151044000-151066800	Weak transcription	Ovary	ovary
12	chr1:151044000-151079600	Weak transcription	Spleen	Spleen
13	chr1:151044000-151080600	Weak transcription	Esophagus	oesophagus
14	chr1:151044200-151047600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:151044200-151049200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:151044200-151069800	Weak transcription	HSMM	muscle
17	chr1:151044200-151070800	Weak transcription	Fetal Lung	lung
18	chr1:151044200-151080200	Weak transcription	Aorta	Aorta
19	chr1:151044400-151047000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:151044400-151047000	Weak transcription	HMEC	breast
21	chr1:151044400-151047200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:151044400-151048400	Weak transcription	HUVEC	blood vessel
23	chr1:151044400-151061600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:151044400-151062200	Weak transcription	Liver	Liver
25	chr1:151044400-151079000	Weak transcription	Left Ventricle	heart
26	chr1:151044400-151079600	Weak transcription	Lung	lung
27	chr1:151044400-151090200	Weak transcription	Gastric	stomach
28	chr1:151044400-151090400	Weak transcription	Right Ventricle	heart
29	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
30	chr1:151044600-151046800	Weak transcription	Thymus	Thymus
31	chr1:151044600-151047000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:151044600-151047000	Weak transcription	NHDF-Ad	bronchial
33	chr1:151044600-151047200	Weak transcription	Fetal Brain Male	brain
34	chr1:151044600-151047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:151044600-151048400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:151044600-151049800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:151044600-151052000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:151044600-151052000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:151044600-151054200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:151044600-151061200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:151044600-151069600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:151044600-151069800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:151044600-151069800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:151044600-151070000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:151044600-151076000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:151044600-151080400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:151044600-151080600	Weak transcription	Brain Anterior Caudate	brain
48	chr1:151044600-151081000	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:151044800-151046800	Weak transcription	NHLF	lung
50	chr1:151044800-151047000	Weak transcription	Duodenum Mucosa	Duodenum

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