Variant report

Variant	rs17677404
Chromosome Location	chr2:173345396-173345397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173345156..173347147-chr2:173350221..173352844,2	K562	blood:
2	chr2:172863090..172865641-chr2:173344065..173346219,2	K562	blood:

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000091409	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10497383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076596	0.82[MEX][hapmap]
rs11883720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11887938	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892037	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11896937	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898822	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12469788	0.81[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap]
rs1344272	0.93[CEU][hapmap]
rs1574258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17286988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17676243	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17676773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17727678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17727732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17739735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17739946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293649	0.93[CEU][hapmap]
rs36002642	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074913	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4405727	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4619573	0.93[CEU][hapmap]
rs4972510	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4972832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972836	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4972837	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55802347	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717877	0.82[CEU][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap]
rs6728123	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746138	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6755605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892573	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72892577	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72892596	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72892601	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72894305	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72894375	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72894389	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72894396	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72894400	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72896105	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7564591	0.93[CEU][hapmap];0.87[TSI][hapmap]
rs7564654	0.93[CEU][hapmap];0.81[TSI][hapmap]
rs7566921	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7582972	0.93[CEU][hapmap]
rs7594889	0.87[CHD][hapmap]
rs7609465	0.93[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17677404	DCAF17	cis	cerebellum	SCAN
rs17677404	HOXD4	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173327200-173353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:173328800-173353400	Weak transcription	Right Ventricle	heart
5	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
6	chr2:173330200-173345600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:173330200-173350400	Weak transcription	Primary B cells from cord blood	blood
8	chr2:173330400-173360400	Weak transcription	Small Intestine	intestine
9	chr2:173330600-173345600	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:173330600-173346400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:173330600-173351400	Weak transcription	Psoas Muscle	Psoas
12	chr2:173330600-173351400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:173330600-173351600	Weak transcription	Brain Anterior Caudate	brain
14	chr2:173330600-173352400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:173330600-173352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:173330600-173352600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:173330600-173353200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:173330600-173353200	Weak transcription	Aorta	Aorta
19	chr2:173330600-173353400	Weak transcription	Fetal Stomach	stomach
20	chr2:173330600-173371400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:173330600-173372200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:173330600-173373200	Strong transcription	NHEK	skin
23	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
27	chr2:173330800-173345400	Weak transcription	NHLF	lung
28	chr2:173330800-173348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:173331000-173346600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:173331000-173348400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:173331000-173370000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:173331000-173373800	Strong transcription	HMEC	breast
35	chr2:173331200-173372000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:173331400-173370200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:173331600-173348800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:173331800-173348000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr2:173332400-173351400	Weak transcription	Spleen	Spleen
40	chr2:173334000-173349600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:173335400-173354000	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:173336000-173346000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:173337800-173360200	Strong transcription	Fetal Thymus	thymus
44	chr2:173338000-173349200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:173340200-173346400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:173341200-173347800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:173341800-173345800	Strong transcription	Thymus	Thymus
48	chr2:173342200-173346400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:173342400-173345400	Strong transcription	Colonic Mucosa	Colon
50	chr2:173342400-173345800	Strong transcription	Fetal Intestine Small	intestine

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