Variant report

Variant	rs6601606
Chromosome Location	chr8:11638244-11638245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11636736..11639024-chr8:11663539..11665876,2	K562	blood:
2	chr8:11636825..11638712-chr8:11641059..11643183,2	K562	blood:
3	chr8:11626972..11629777-chr8:11636747..11639183,2	MCF-7	breast:
4	chr8:11637260..11639168-chr8:11645099..11647488,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079459	Chromatin interaction
ENSG00000154328	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1534862	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs17153776	0.91[EUR][1000 genomes]
rs17524895	0.86[EUR][1000 genomes]
rs2740439	0.88[ASN][1000 genomes]
rs28438570	0.83[EUR][1000 genomes]
rs4639	0.84[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs59648461	0.83[EUR][1000 genomes]
rs67631516	0.86[ASN][1000 genomes]
rs6993013	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8191530	1.00[EUR][1000 genomes]
rs8191547	0.93[CHB][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8191579	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8191581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8191585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8191593	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8191600	0.93[ASN][1000 genomes]
rs8191602	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8191609	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8191613	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8191614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8191618	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8191624	1.00[EUR][1000 genomes]
rs8191631	0.96[ASN][1000 genomes]
rs8191634	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8191636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8191640	0.95[EUR][1000 genomes]
rs8191652	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8191664	1.00[EUR][1000 genomes]
rs8191678	0.87[ASN][1000 genomes]
rs904015	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv890360	chr8:11619163-11639991	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Neutrophil count	21507922	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6601606	NEIL2	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11628000-11640800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:11628400-11640000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr8:11628400-11640600	Weak transcription	A549	lung
4	chr8:11628400-11640600	Weak transcription	NH-A	brain
5	chr8:11628400-11641200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr8:11628400-11641200	Weak transcription	Psoas Muscle	Psoas
7	chr8:11628400-11641400	Weak transcription	Esophagus	oesophagus
8	chr8:11628400-11647200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr8:11628400-11653000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr8:11628400-11656800	Weak transcription	Small Intestine	intestine
11	chr8:11628600-11638400	Weak transcription	NHLF	lung
12	chr8:11628600-11638800	Weak transcription	HMEC	breast
13	chr8:11628600-11640600	Weak transcription	Osteobl	bone
14	chr8:11628600-11640800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr8:11628600-11641800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr8:11628600-11647200	Weak transcription	Fetal Heart	heart
17	chr8:11628800-11639800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr8:11628800-11640200	Weak transcription	Pancreas	Pancrea
19	chr8:11628800-11640400	Weak transcription	HSMMtube	muscle
20	chr8:11628800-11640600	Weak transcription	Placenta	Placenta
21	chr8:11628800-11640600	Weak transcription	HepG2	liver
22	chr8:11628800-11640800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr8:11628800-11640800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr8:11628800-11641000	Weak transcription	Colon Smooth Muscle	Colon
25	chr8:11628800-11641200	Weak transcription	HSMM	muscle
26	chr8:11628800-11641600	Weak transcription	Colonic Mucosa	Colon
27	chr8:11628800-11646800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr8:11629000-11640200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr8:11629000-11640400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr8:11629000-11640800	Weak transcription	Gastric	stomach
31	chr8:11629000-11640800	Weak transcription	Right Ventricle	heart
32	chr8:11629000-11641000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr8:11629000-11641600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr8:11629200-11640200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr8:11629200-11640800	Weak transcription	Fetal Intestine Large	intestine
36	chr8:11629200-11644200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr8:11629400-11638800	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr8:11629400-11640000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr8:11629400-11640400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr8:11629400-11640400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr8:11629600-11638400	Strong transcription	Fetal Muscle Leg	muscle
42	chr8:11629600-11645800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr8:11629800-11638600	Strong transcription	Primary T cells from cord blood	blood
44	chr8:11629800-11644200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr8:11630600-11640800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr8:11631200-11640200	Weak transcription	Brain Substantia Nigra	brain
47	chr8:11632000-11640400	Weak transcription	Fetal Brain Male	brain
48	chr8:11632000-11641800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr8:11632200-11641000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr8:11633000-11640800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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