Variant report

Variant	rs10402946
Chromosome Location	chr19:44139182-44139183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44118551..44131201-chr19:44135615..44147023,20	K562	blood:
2	chr19:44137719..44140968-chr19:44143779..44146141,3	K562	blood:
3	chr19:44138850..44140610-chr19:44142090..44144067,2	MCF-7	breast:
4	chr19:44137846..44140396-chr19:44141392..44144288,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131116	Chromatin interaction
ENSG00000105767	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13343696	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17655646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs184239	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs2030404	0.88[CHD][hapmap]
rs2270075	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2599462	0.88[CHD][hapmap]
rs2682563	0.88[CHD][hapmap]
rs2682585	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs2682586	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2854501	0.87[CHD][hapmap]
rs2854506	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs2854508	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs2854509	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs304719	0.85[ASW][hapmap];0.97[LWK][hapmap];0.83[YRI][hapmap]
rs304720	0.85[ASW][hapmap];0.97[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs304722	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs304723	0.92[ASW][hapmap];0.97[LWK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs304731	1.00[CHB][hapmap]
rs3213255	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs3213263	0.83[CHD][hapmap]
rs3213334	0.88[CHD][hapmap]
rs3213356	0.88[CHD][hapmap]
rs34163641	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34521657	0.84[AFR][1000 genomes]
rs34637472	0.92[ASW][hapmap];0.97[LWK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs365063	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs3803910	0.84[AFR][1000 genomes]
rs427115	0.85[ASW][hapmap];0.91[LWK][hapmap];0.88[YRI][hapmap]
rs4803646	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251275	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762506	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs762507	0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10402946	ETHE1	cis	lymphoblastoid	seeQTL
rs10402946	CCDC8	cis	parietal	SCAN
rs10402946	ELSPBP1	cis	cerebellum	SCAN
rs10402946	STRN4	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44124600-44143400	Weak transcription	Right Atrium	heart
2	chr19:44125000-44139200	Weak transcription	Pancreas	Pancrea
3	chr19:44131200-44139400	Weak transcription	Spleen	Spleen
4	chr19:44137400-44142600	Enhancers	Fetal Brain Male	brain
5	chr19:44138200-44139800	Bivalent Enhancer	Fetal Thymus	thymus
6	chr19:44138200-44140400	Enhancers	NHDF-Ad	bronchial
7	chr19:44138200-44140600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:44138200-44140800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:44138200-44140800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:44138200-44140800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:44138400-44139200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:44138400-44139200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:44138400-44139200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:44138400-44139400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:44138400-44139600	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr19:44138400-44140800	Enhancers	A549	lung
17	chr19:44138600-44140000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr19:44138600-44140200	Active TSS	Brain Angular Gyrus	brain
19	chr19:44138600-44140200	Active TSS	Brain Hippocampus Middle	brain
20	chr19:44138600-44140800	Active TSS	Brain Substantia Nigra	brain
21	chr19:44138600-44140800	Enhancers	HMEC	breast
22	chr19:44138800-44139200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:44138800-44139200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr19:44138800-44139200	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr19:44138800-44139200	Enhancers	NHEK	skin
26	chr19:44138800-44139200	Bivalent Enhancer	NHLF	lung
27	chr19:44138800-44139600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:44138800-44139600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:44138800-44139600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:44138800-44139600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:44138800-44139600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
32	chr19:44138800-44139600	Flanking Active TSS	Osteobl	bone
33	chr19:44138800-44139800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr19:44138800-44139800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr19:44138800-44139800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr19:44138800-44139800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:44138800-44139800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr19:44138800-44139800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:44138800-44139800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:44138800-44139800	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr19:44138800-44139800	Active TSS	Fetal Kidney	kidney
42	chr19:44138800-44139800	Active TSS	Rectal Smooth Muscle	rectum
43	chr19:44138800-44140000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr19:44138800-44140000	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr19:44138800-44140000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr19:44138800-44140200	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr19:44138800-44140400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:44138800-44140400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:44138800-44140600	Active TSS	Brain Anterior Caudate	brain
50	chr19:44138800-44140600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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