Variant report

Variant	rs2857634
Chromosome Location	chr22:30008750-30008751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30007746..30010687-chr22:30014931..30018872,3	K562	blood:
2	chr22:29999599..30001910-chr22:30007013..30009061,2	K562	blood:
3	chr22:29999797..30002683-chr22:30006391..30009061,4	K562	blood:

Variant related genes	Relation type
ENSG00000186575	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1009147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs105268	1.00[JPT][hapmap]
rs11090576	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs165602	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs165607	1.00[JPT][hapmap]
rs165624	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs165633	1.00[JPT][hapmap]
rs165649	1.00[JPT][hapmap]
rs165734	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs165821	1.00[JPT][hapmap]
rs165853	0.84[ASN][1000 genomes]
rs17460259	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17462054	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs174649	1.00[JPT][hapmap]
rs174718	1.00[JPT][hapmap]
rs1800540	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970776	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2008880	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.85[ASN][1000 genomes]
rs2079339	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2079648	0.82[AMR][1000 genomes]
rs2530660	0.92[ASN][1000 genomes]
rs457930	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs465736	1.00[JPT][hapmap]
rs467669	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs467768	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs468563	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs469189	0.85[ASN][1000 genomes]
rs4823046	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs4823048	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752917	1.00[JPT][hapmap]
rs5763315	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs5763347	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5763348	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs5997506	0.82[EUR][1000 genomes]
rs6006219	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6006225	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73159014	0.85[ASN][1000 genomes]
rs73390944	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs737979	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8135737	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9625852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised 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	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2857634	C22orf13	cis	parietal	SCAN
rs2857634	SEC14L4	cis	cerebellum	SCAN
rs2857634	EIF2B2	trans	lymphoblastoid	seeQTL
rs2857634	NEFH	cis	multi-tissue	Pritchard
rs2857634	SGSM1	cis	cerebellum	SCAN
rs2857634	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30026600	Weak transcription	Gastric	stomach
2	chr22:30001000-30013400	Weak transcription	Fetal Kidney	kidney
3	chr22:30001000-30019400	Weak transcription	Thymus	Thymus
4	chr22:30001200-30013800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr22:30001400-30013400	Weak transcription	Brain Angular Gyrus	brain
6	chr22:30001400-30013400	Weak transcription	Ovary	ovary
7	chr22:30001400-30013400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr22:30001400-30014000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr22:30001600-30013400	Weak transcription	Fetal Lung	lung
10	chr22:30001600-30013600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr22:30002000-30013400	Weak transcription	Small Intestine	intestine
12	chr22:30002000-30014200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr22:30002000-30017600	Weak transcription	Primary T cells from cord blood	blood
14	chr22:30002200-30013600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr22:30002400-30011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr22:30002400-30011600	Weak transcription	NHLF	lung
17	chr22:30002400-30013000	Weak transcription	HMEC	breast
18	chr22:30002400-30013600	Weak transcription	HSMMtube	muscle
19	chr22:30002400-30013800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr22:30002600-30011200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr22:30002600-30013400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr22:30002600-30013400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr22:30002600-30013400	Weak transcription	Colon Smooth Muscle	Colon
24	chr22:30002600-30013400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr22:30002600-30013400	Weak transcription	HSMM	muscle
26	chr22:30002600-30014000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr22:30002800-30013600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr22:30002800-30017600	Weak transcription	Lung	lung
29	chr22:30003000-30013400	Weak transcription	Pancreas	Pancrea
30	chr22:30003000-30013400	Weak transcription	Psoas Muscle	Psoas
31	chr22:30003000-30016600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr22:30003200-30013200	Weak transcription	NHDF-Ad	bronchial
33	chr22:30003200-30014000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr22:30003400-30010600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr22:30003400-30013800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr22:30003400-30014000	Weak transcription	Right Atrium	heart
37	chr22:30003400-30017200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr22:30003600-30011200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr22:30003600-30011400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr22:30003600-30013200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr22:30003600-30014000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr22:30003600-30016400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr22:30003800-30013600	Weak transcription	Osteobl	bone
44	chr22:30003800-30032800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr22:30005000-30013800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr22:30005200-30019400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr22:30005400-30011000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr22:30005400-30017800	Weak transcription	Primary B cells from cord blood	blood
49	chr22:30005600-30010600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr22:30005600-30013200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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