Variant report

Variant	rs3798557
Chromosome Location	chr6:34310476-34310477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34308267..34311502-chr6:34313780..34316538,3	K562	blood:
2	chr6:34309301..34312552-chr6:34312659..34315940,4	K562	blood:
3	chr6:34214571..34216737-chr6:34309233..34311711,2	K562	blood:
4	chr6:34238995..34241541-chr6:34307534..34310949,3	K562	blood:
5	chr6:34303920..34306349-chr6:34307899..34311010,3	K562	blood:
6	chr6:34305250..34307284-chr6:34307723..34310637,2	MCF-7	breast:
7	chr6:34307128..34308911-chr6:34309143..34310713,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10484267	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10484268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1057691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1060308	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10648	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1127084	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1265	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12654	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13466	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883137	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883475	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883896	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16888452	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17628798	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17628946	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629180	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696829	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1994923	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs206922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3798554	0.80[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3798558	1.00[YRI][hapmap]
rs41269032	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41269034	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269036	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269038	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4713771	0.87[EUR][1000 genomes]
rs55674397	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55684754	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55694290	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55763242	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55779010	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55798596	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55812200	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55833185	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55863933	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55864834	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56033036	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56039915	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56107559	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56188036	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56274913	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56309550	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56323997	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56330729	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59832183	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62399870	0.85[EUR][1000 genomes]
rs6911272	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7738665	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7760373	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7770443	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs875274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9368811	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	esv1797588	chr6:34310476-34319041	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3798557	NUDT3	cis	parietal	SCAN
rs3798557	NUDT3	Cis_1M	lymphoblastoid	RTeQTL
rs3798557	NUDT3	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:34284800-34310800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:34285200-34330600	Weak transcription	Thymus	Thymus
4	chr6:34285800-34326600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:34289000-34325200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:34297400-34312800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:34298600-34326400	Weak transcription	A549	lung
8	chr6:34299400-34310800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:34301600-34318000	Weak transcription	Fetal Brain Female	brain
10	chr6:34303000-34312800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:34304600-34310600	Enhancers	Rectal Smooth Muscle	rectum
12	chr6:34305000-34310600	Enhancers	Fetal Heart	heart
13	chr6:34305400-34311200	Enhancers	Psoas Muscle	Psoas
14	chr6:34306000-34313800	Weak transcription	NHEK	skin
15	chr6:34306000-34327800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:34306000-34328800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:34306200-34311000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:34306400-34310800	Strong transcription	Primary T cells from cord blood	blood
19	chr6:34306400-34310800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:34306600-34310600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:34306600-34312200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:34307000-34311000	Weak transcription	Spleen	Spleen
23	chr6:34307000-34312400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:34307000-34320000	Weak transcription	Ovary	ovary
25	chr6:34307400-34314200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:34307600-34310800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr6:34308000-34310800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:34308200-34310600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr6:34308400-34310800	Enhancers	Brain Substantia Nigra	brain
30	chr6:34308400-34312400	Enhancers	HUVEC	blood vessel
31	chr6:34308600-34310800	Enhancers	Brain Anterior Caudate	brain
32	chr6:34308800-34310600	Enhancers	Fetal Kidney	kidney
33	chr6:34308800-34313600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr6:34308800-34330800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:34309000-34311800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:34309200-34310600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:34309200-34315800	Weak transcription	Placenta	Placenta
38	chr6:34309200-34318200	Weak transcription	Fetal Lung	lung
39	chr6:34309400-34310800	Enhancers	Right Atrium	heart
40	chr6:34309400-34310800	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr6:34309400-34311400	Enhancers	Left Ventricle	heart
42	chr6:34309400-34312000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:34309400-34317200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:34309400-34317800	Weak transcription	Brain Germinal Matrix	brain
45	chr6:34309600-34310800	Strong transcription	K562	blood
46	chr6:34309600-34311200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:34309600-34311400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:34309600-34314800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:34309600-34317200	Weak transcription	NHDF-Ad	bronchial
50	chr6:34309600-34319800	Weak transcription	Small Intestine	intestine

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