Variant report

Variant	rs3798859
Chromosome Location	chr6:127663116-127663117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:127638086..127642248-chr6:127662682..127665372,3	K562	blood:
2	chr6:127586572..127589762-chr6:127662304..127666058,6	K562	blood:
3	chr6:127638086..127640827-chr6:127662682..127665250,2	K562	blood:
4	chr6:127586417..127590637-chr6:127662350..127666578,4	K562	blood:
5	chr6:127647745..127649356-chr6:127662389..127665188,2	K562	blood:

Variant related genes	Relation type
ENSG00000118518	Chromatin interaction
ENSG00000251768	Chromatin interaction
ENSG00000093144	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11154395	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11154396	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11154397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11154398	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11556354	0.81[CEU][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs11961994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199451	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12210968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12212752	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12215298	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12529077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13192350	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13215850	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2057224	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2180341	0.84[TSI][hapmap]
rs2326567	0.84[TSI][hapmap]
rs2875981	0.81[ASW][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3756993	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798853	0.84[TSI][hapmap]
rs4502958	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4577822	0.80[AFR][1000 genomes]
rs4897207	0.81[TSI][hapmap]
rs6569479	0.84[TSI][hapmap]
rs6683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6933893	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7453272	0.84[TSI][hapmap]
rs7775667	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7776136	0.84[TSI][hapmap]
rs877102	0.93[GIH][hapmap];0.92[TSI][hapmap]
rs9398840	0.81[TSI][hapmap]
rs9401953	0.81[TSI][hapmap]

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	nsv604641	chr6:127657099-127719062	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3798859	ECHDC1	Cis_1M	lymphoblastoid	RTeQTL
rs3798859	NKAIN2	cis	parietal	SCAN
rs3798859	ECHDC1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:127608800-127663600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:127608800-127663600	Weak transcription	Gastric	stomach
3	chr6:127648000-127663200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:127657600-127663400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr6:127657800-127663600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr6:127658800-127663200	Enhancers	Liver	Liver
7	chr6:127659200-127663200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr6:127659200-127663400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:127659600-127663200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:127660200-127663200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:127660200-127663600	Enhancers	Primary B cells from peripheral blood	blood
12	chr6:127660800-127663600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:127661200-127664000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:127661400-127663400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr6:127661600-127663200	Enhancers	Fetal Intestine Small	intestine
16	chr6:127661600-127666000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr6:127661800-127663200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:127661800-127663200	Weak transcription	Placenta	Placenta
19	chr6:127661800-127663400	Weak transcription	Left Ventricle	heart
20	chr6:127661800-127663400	Weak transcription	Pancreas	Pancrea
21	chr6:127661800-127663400	Weak transcription	Right Ventricle	heart
22	chr6:127661800-127663600	Weak transcription	Esophagus	oesophagus
23	chr6:127661800-127664000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:127662000-127663400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:127662000-127663400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr6:127662000-127664000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:127662000-127665600	Active TSS	Right Atrium	heart
28	chr6:127662200-127663400	Enhancers	Stomach Mucosa	stomach
29	chr6:127662200-127663400	Weak transcription	Spleen	Spleen
30	chr6:127662200-127663600	Flanking Active TSS	HMEC	breast
31	chr6:127662200-127663800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr6:127662400-127663200	Flanking Active TSS	GM12878-XiMat	blood
33	chr6:127662400-127663400	Flanking Active TSS	HepG2	liver
34	chr6:127662400-127663800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr6:127662400-127663800	Flanking Active TSS	Fetal Brain Female	brain
36	chr6:127662400-127664000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr6:127662600-127663200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:127662600-127663200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr6:127662600-127663200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr6:127662600-127663200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:127662600-127663200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:127662600-127663200	Enhancers	Brain Anterior Caudate	brain
43	chr6:127662600-127663400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:127662600-127663400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:127662600-127663400	Enhancers	Fetal Thymus	thymus
46	chr6:127662600-127663600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr6:127662600-127663600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:127662600-127663600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr6:127662600-127663600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:127662600-127663600	Enhancers	Small Intestine	intestine

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