Variant report

Variant	rs11962015
Chromosome Location	chr6:5618987-5618988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5618499..5620610-chr6:5626693..5628979,2	K562	blood:
2	chr6:5609969..5611663-chr6:5617459..5619947,2	K562	blood:
3	chr6:5618457..5621513-chr6:5623126..5626638,4	K562	blood:

Variant related genes	Relation type
ENSG00000218574	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11755552	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs11756138	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[TSI][hapmap];0.93[ASN][1000 genomes]
rs11964159	1.00[CHB][hapmap]
rs17133295	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs1983564	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2064106	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2064107	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4323358	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs55762144	0.93[ASN][1000 genomes]
rs56276929	0.93[ASN][1000 genomes]
rs57607452	0.93[ASN][1000 genomes]
rs60671092	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61526984	0.93[ASN][1000 genomes]
rs6904473	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911625	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6918207	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935073	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs6936430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72817799	0.93[ASN][1000 genomes]
rs760676	0.93[ASN][1000 genomes]
rs760677	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs7738833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs7751107	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769150	0.93[ASN][1000 genomes]
rs926312	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs9378974	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9502321	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs9502322	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs9504442	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs9504443	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs9504444	0.93[ASN][1000 genomes]
rs9504445	0.93[ASN][1000 genomes]
rs9504447	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs9504448	0.93[ASN][1000 genomes]
rs9504449	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs9504450	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs9504451	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs9504452	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs9504454	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1016905	chr6:5566364-5639167	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1015549	chr6:5593965-5630468	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11962015	ARL4C	trans	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5577400-5639800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5581000-5640400	Weak transcription	Gastric	stomach
3	chr6:5587200-5619400	Weak transcription	Primary B cells from cord blood	blood
4	chr6:5590800-5622000	Weak transcription	Right Atrium	heart
5	chr6:5591200-5619000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:5591600-5626400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:5592200-5619200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:5593400-5621000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:5605600-5619200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:5610400-5620200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:5610600-5641000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:5612000-5619200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:5612200-5622200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:5612400-5628000	Weak transcription	Fetal Intestine Large	intestine
15	chr6:5612600-5640000	Weak transcription	Fetal Stomach	stomach
16	chr6:5612800-5626800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:5613000-5627200	Weak transcription	Adipose Nuclei	Adipose
18	chr6:5613200-5640400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:5613600-5627000	Weak transcription	Dnd41	blood
20	chr6:5613800-5619200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr6:5614400-5619200	Weak transcription	Fetal Thymus	thymus
22	chr6:5614400-5639000	Weak transcription	Lung	lung
23	chr6:5614600-5619200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:5614600-5621200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:5614600-5626800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:5614600-5628200	Weak transcription	Ovary	ovary
27	chr6:5614600-5636600	Weak transcription	Pancreas	Pancrea
28	chr6:5614600-5640000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:5614600-5640400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:5615400-5619000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:5615600-5624200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:5616200-5627000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:5617000-5619400	Enhancers	Fetal Heart	heart
34	chr6:5617400-5619600	Weak transcription	Aorta	Aorta
35	chr6:5617800-5625600	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:5618000-5619000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:5618600-5619000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:5618600-5622800	Weak transcription	Left Ventricle	heart
39	chr6:5618800-5619400	Enhancers	Primary T cells from cord blood	blood
40	chr6:5618800-5620400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:5618800-5624000	Weak transcription	Right Ventricle	heart

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