Variant report

Variant	rs17246404
Chromosome Location	chr7:124462661-124462662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:124404262..124405820-chr7:124460422..124463295,2	K562	blood:

Variant related genes	Relation type
ENSG00000170775	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1009450	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap]
rs10224463	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10225552	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226033	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10228201	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230610	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10233385	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10233596	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10240673	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10241173	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10244817	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246424	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10249722	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10253613	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10264060	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10265763	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10268372	0.81[ASN][1000 genomes]
rs10271646	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10281582	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10464529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12111865	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1525613	0.91[CEU][hapmap]
rs1541416	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17325193	0.95[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs2107939	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2170352	0.91[CEU][hapmap]
rs2239532	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286175	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2402751	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2402752	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28523990	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28622327	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28638102	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28728448	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28844358	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34986416	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36045816	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3925331	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473974	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4532534	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55964341	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56313563	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56321835	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56356267	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56387611	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59237623	0.84[AMR][1000 genomes]
rs59294613	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59670428	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66492217	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66513837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66526112	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66665074	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66922607	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67084428	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67146030	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67552763	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67585224	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67939974	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68007199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68091803	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6943653	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6952721	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6971909	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs720613	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720614	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs722560	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs727505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7777947	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7790856	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7791430	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7795943	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7801661	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];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7806680	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9655845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs988699	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs989177	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	esv3446198	chr7:124358002-124586856	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv889134	chr7:124462081-124552802	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv889135	chr7:124462081-124584834	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Chronic lymphocytic leukemia	24292274	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17246404	IMPDH1	cis	parietal	SCAN
rs17246404	WASL	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124445000-124463800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr7:124450800-124467000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:124451400-124463600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr7:124451600-124466600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:124452800-124475000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:124454400-124463000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:124454400-124463000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:124454400-124497600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:124454600-124463800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:124454600-124501400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:124457600-124497600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:124458800-124463600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:124459000-124463600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:124459000-124463800	Weak transcription	Left Ventricle	heart
15	chr7:124459000-124463800	Weak transcription	GM12878-XiMat	blood
16	chr7:124459000-124497800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:124459200-124467600	Weak transcription	Esophagus	oesophagus
18	chr7:124459200-124469000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:124459200-124497600	Weak transcription	Pancreas	Pancrea
20	chr7:124459200-124499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:124459400-124463000	Weak transcription	Fetal Thymus	thymus
22	chr7:124459400-124497600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:124459400-124497600	Weak transcription	Brain Anterior Caudate	brain
24	chr7:124459600-124463200	Weak transcription	Ovary	ovary
25	chr7:124460200-124463200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr7:124460200-124463800	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:124460200-124463800	Weak transcription	HUVEC	blood vessel
28	chr7:124460200-124465800	Weak transcription	NH-A	brain
29	chr7:124460200-124466000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:124460200-124483400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:124460400-124463000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:124460400-124463000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:124460400-124488600	Weak transcription	HSMMtube	muscle
34	chr7:124460600-124463800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:124460600-124486200	Weak transcription	Brain Substantia Nigra	brain
36	chr7:124460800-124476200	Weak transcription	Fetal Brain Male	brain
37	chr7:124461000-124499200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr7:124461000-124499600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr7:124461200-124463800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:124461200-124465800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr7:124461400-124463000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr7:124461400-124463400	Weak transcription	Placenta	Placenta
43	chr7:124461400-124463600	Weak transcription	Fetal Kidney	kidney
44	chr7:124461400-124463800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:124461400-124463800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:124461400-124530800	Weak transcription	NHDF-Ad	bronchial
47	chr7:124461600-124464400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr7:124461600-124466600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr7:124461600-124466800	Strong transcription	Liver	Liver
50	chr7:124461600-124467200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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