Variant report

Variant	rs905594
Chromosome Location	chr1:161741274-161741275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161734589..161736537-chr1:161741114..161743085,3	K562	blood:
2	chr1:161736308..161738165-chr1:161740063..161741622,2	MCF-7	breast:
3	chr1:161739606..161743338-chr1:161743718..161745860,3	K562	blood:

Variant related genes	Relation type
ENSG00000118217	Chromatin interaction
ENSG00000226889	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1006310	0.90[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1027700	0.80[ASN][1000 genomes]
rs1058405	0.80[ASN][1000 genomes]
rs10753686	0.83[MEX][hapmap];0.84[TSI][hapmap]
rs10918137	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12124509	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1847383	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2257107	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2340720	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2340721	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2499854	0.81[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap]
rs3820449	0.80[CHD][hapmap]
rs4656336	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61802510	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666482	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683830	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6695760	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7519514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931778	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs905594	FCRLM2	cis	multi-tissue	Pritchard
rs905594	ATF6	cis	lymphoblastoid	seeQTL
rs905594	ATF6	Cis_1M	lymphoblastoid	RTeQTL
rs905594	NTRK1	cis	parietal	SCAN
rs905594	FCRLA	Cis_1M	lymphoblastoid	RTeQTL
rs905594	ACTL7B	trans	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161736800-161752000	Weak transcription	Lung	lung
2	chr1:161736800-161754000	Weak transcription	Colonic Mucosa	Colon
3	chr1:161736800-161757200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:161737000-161743800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:161737000-161745400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:161737000-161751600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:161737000-161752000	Weak transcription	Left Ventricle	heart
8	chr1:161737000-161765600	Weak transcription	Aorta	Aorta
9	chr1:161737200-161741400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:161737200-161741600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:161737200-161744000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:161737200-161745000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:161737200-161746600	Weak transcription	NHLF	lung
14	chr1:161737200-161748000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:161737200-161751200	Weak transcription	Placenta	Placenta
16	chr1:161737200-161751400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:161737200-161752200	Weak transcription	Psoas Muscle	Psoas
18	chr1:161737200-161752600	Weak transcription	Esophagus	oesophagus
19	chr1:161737200-161752800	Weak transcription	HSMMtube	muscle
20	chr1:161737200-161761600	Weak transcription	Fetal Brain Male	brain
21	chr1:161737200-161761600	Weak transcription	Right Ventricle	heart
22	chr1:161737200-161775200	Weak transcription	Fetal Stomach	stomach
23	chr1:161737200-161775800	Weak transcription	Stomach Mucosa	stomach
24	chr1:161737200-161780000	Weak transcription	Fetal Intestine Small	intestine
25	chr1:161737400-161750400	Weak transcription	Fetal Intestine Large	intestine
26	chr1:161737400-161751400	Weak transcription	Osteobl	bone
27	chr1:161737400-161752200	Weak transcription	HSMM	muscle
28	chr1:161737600-161741400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:161737600-161745400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:161737600-161751400	Weak transcription	NHDF-Ad	bronchial
31	chr1:161737600-161752000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:161737600-161762000	Weak transcription	Fetal Lung	lung
33	chr1:161737600-161764600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:161737800-161750400	Weak transcription	Brain Germinal Matrix	brain
35	chr1:161738000-161752400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:161738200-161741800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:161738200-161743400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:161738200-161752200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:161738200-161753600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:161738200-161760200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:161738400-161741400	Weak transcription	Adipose Nuclei	Adipose
42	chr1:161738400-161751200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:161738400-161754000	Weak transcription	Fetal Brain Female	brain
44	chr1:161738600-161741600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:161738600-161741800	Enhancers	Dnd41	blood
46	chr1:161738600-161743400	Weak transcription	Hela-S3	cervix
47	chr1:161738600-161747600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:161738600-161752200	Weak transcription	HepG2	liver
49	chr1:161738600-161752600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:161738600-161753800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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