Variant report

Variant	rs3819976
Chromosome Location	chr1:241695792-241695793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241693526..241696085-chr1:241801417..241805051,3	MCF-7	breast:
2	chr1:241692902..241697485-chr1:242010276..242014432,6	K562	blood:
3	chr1:241693547..241697485-chr1:242010276..242012986,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR64-2	chr1:241695679-241695798	NONHSAT010548

Variant related genes	Relation type
ENSG00000054277	Chromatin interaction
ENSG00000174371	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10802969	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926505	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10926508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926510	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064150	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076255	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079341	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841808	0.87[EUR][1000 genomes]
rs3765802	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765804	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4659609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660101	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56957678	0.87[EUR][1000 genomes]
rs58766151	0.87[EUR][1000 genomes]
rs61543265	0.87[EUR][1000 genomes]
rs6429277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66482665	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66497254	0.87[EUR][1000 genomes]
rs66669018	0.87[EUR][1000 genomes]
rs66710178	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6678986	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs6679186	0.87[EUR][1000 genomes]
rs6681649	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684064	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687609	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6690411	0.87[EUR][1000 genomes]
rs6698519	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67267325	0.87[EUR][1000 genomes]
rs67439618	0.87[EUR][1000 genomes]
rs68147305	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72766004	0.87[EUR][1000 genomes]
rs73137530	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539730	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3819976	KMO	cis	lymphoblastoid	seeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241694400-241696600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:241694600-241695800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:241694600-241695800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:241694600-241695800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:241694600-241695800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:241694600-241695800	Active TSS	Brain Angular Gyrus	brain
7	chr1:241694600-241695800	Active TSS	Colonic Mucosa	Colon
8	chr1:241694600-241695800	Active TSS	Colon Smooth Muscle	Colon
9	chr1:241694600-241695800	Active TSS	Fetal Brain Male	brain
10	chr1:241694600-241695800	Active TSS	Fetal Intestine Small	intestine
11	chr1:241694600-241695800	Active TSS	Fetal Thymus	thymus
12	chr1:241694600-241695800	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr1:241694600-241696000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:241694600-241696200	Active TSS	Liver	Liver
15	chr1:241694600-241696200	Active TSS	GM12878-XiMat	blood
16	chr1:241694600-241696400	Active TSS	Brain Substantia Nigra	brain
17	chr1:241694600-241697000	Active TSS	Duodenum Mucosa	Duodenum
18	chr1:241694600-241697200	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr1:241694800-241695800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:241694800-241695800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:241694800-241695800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:241694800-241695800	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr1:241694800-241695800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:241694800-241695800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:241694800-241695800	Active TSS	Brain Germinal Matrix	brain
26	chr1:241694800-241695800	Active TSS	Fetal Intestine Large	intestine
27	chr1:241694800-241695800	Active TSS	Rectal Smooth Muscle	rectum
28	chr1:241694800-241695800	Active TSS	Right Atrium	heart
29	chr1:241694800-241695800	Active TSS	NHDF-Ad	bronchial
30	chr1:241694800-241696200	Active TSS	Primary monocytes fromperipheralblood	blood
31	chr1:241694800-241696400	Active TSS	Adipose Nuclei	Adipose
32	chr1:241694800-241696400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr1:241694800-241696600	Active TSS	Primary B cells from peripheral blood	blood
34	chr1:241694800-241697000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:241694800-241697400	Active TSS	Fetal Kidney	kidney
36	chr1:241694800-241697600	Active TSS	Placenta	Placenta
37	chr1:241695000-241695800	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr1:241695200-241695800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr1:241695400-241695800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:241695400-241695800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:241695400-241695800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:241695400-241695800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr1:241695400-241695800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr1:241695400-241695800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr1:241695400-241695800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr1:241695400-241695800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:241695400-241695800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr1:241695400-241695800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr1:241695400-241695800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:241695400-241695800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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