Variant report

Variant	rs2047987
Chromosome Location	chr4:76834545-76834546
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	chr4:76833793..76835849-chr4:76861074..76863584,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138744	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10155195	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10518142	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs11490704	0.83[ASN][1000 genomes]
rs1876096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2135232	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs2280101	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28759823	0.86[ASN][1000 genomes]
rs55967764	0.84[ASN][1000 genomes]
rs58317633	0.86[ASN][1000 genomes]
rs6823734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72651374	0.86[ASN][1000 genomes]
rs7686066	0.83[ASN][1000 genomes]
rs905958	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS 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 miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2047987	ASAHL	cis	multi-tissue	Pritchard
rs2047987	SLC6A20	trans	multi-tissue	Pritchard
rs2047987	CDKL2	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76823000-76836600	Weak transcription	Spleen	Spleen
2	chr4:76823600-76835000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr4:76823800-76835000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:76824000-76835200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:76824800-76841000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:76827600-76841000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:76827800-76836600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:76829400-76835000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:76829400-76836600	Weak transcription	Placenta	Placenta
10	chr4:76829400-76836600	Weak transcription	Ovary	ovary
11	chr4:76830000-76837000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:76830200-76835000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:76830200-76839600	Weak transcription	Primary B cells from cord blood	blood
14	chr4:76830400-76838200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:76830400-76838600	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:76830600-76838200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:76830800-76836000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:76830800-76836800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:76831000-76840800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:76831600-76841800	Weak transcription	NHDF-Ad	bronchial
21	chr4:76832000-76834600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:76832200-76835800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:76832400-76835000	Weak transcription	Liver	Liver
24	chr4:76832400-76841000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:76832600-76859000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr4:76832800-76835000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:76832800-76838400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:76832800-76838400	Weak transcription	Adipose Nuclei	Adipose
29	chr4:76832800-76838400	Weak transcription	Fetal Intestine Large	intestine
30	chr4:76833000-76838200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:76833000-76841000	Weak transcription	Dnd41	blood
32	chr4:76833000-76842000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:76833400-76836200	Weak transcription	Fetal Intestine Small	intestine
34	chr4:76833400-76836600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:76833400-76841000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:76833400-76841000	Weak transcription	Hela-S3	cervix
37	chr4:76833600-76836600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr4:76833600-76837000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:76833800-76837400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr4:76833800-76838400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr4:76833800-76851200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:76833800-76856400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr4:76833800-76860800	Weak transcription	Fetal Heart	heart
44	chr4:76834000-76834600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr4:76834000-76834600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:76834000-76835800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr4:76834000-76841000	Weak transcription	Aorta	Aorta
48	chr4:76834000-76847000	Strong transcription	Primary T cells from cord blood	blood
49	chr4:76834200-76834600	Enhancers	HSMMtube	muscle
50	chr4:76834200-76835400	Strong transcription	Rectal Mucosa Donor 31	rectum

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