Variant report

Variant	rs12568757
Chromosome Location	chr1:150729793-150729794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150725025..150727549-chr1:150728831..150731687,2	K562	blood:
2	chr1:150638939..150641718-chr1:150729032..150731135,2	K562	blood:
3	chr1:150718367..150722446-chr1:150727232..150730438,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 37 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1053732	0.86[YRI][hapmap]
rs10888388	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11204680	0.81[CHD][hapmap]
rs11204684	0.84[CHD][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap]
rs11204693	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11204695	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11204702	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11204712	0.90[ASN][1000 genomes]
rs11204725	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204735	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs11204737	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs1136774	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11800059	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12125650	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12130363	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12403609	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12725806	0.87[EUR][1000 genomes]
rs12758227	0.83[EUR][1000 genomes]
rs1971378	0.82[CHD][hapmap];0.86[YRI][hapmap]
rs2039590	0.87[EUR][1000 genomes]
rs2048558	0.81[CHD][hapmap]
rs2089081	0.86[EUR][1000 genomes]
rs34002273	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs486836	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4970924	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4970926	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4970976	0.83[EUR][1000 genomes]
rs6587520	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694531	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7520022	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7534124	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9733	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872417	chr1:150618632-150759979	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv872419	chr1:150699199-150738759	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv1008381	chr1:150721254-150745558	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs12568757	FLG	cis	cerebellum	SCAN
rs12568757	HORMAD1	cis	lesional skin	skin_eQTL
rs12568757	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs12568757	HORMAD1	cis	Nerve Tibial	GTEx
rs12568757	RP11-316M1.12	cis	Artery Tibial	GTEx
rs12568757	CTSK	cis	lymphoblastoid	seeQTL
rs12568757	HORMAD1	cis	uninvolved skin	skin_eQTL
rs12568757	ARNT	cis	multi-tissue	Pritchard
rs12568757	PSMD4	cis	parietal	SCAN
rs12568757	ARNT	cis	parietal	SCAN
rs12568757	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs12568757	ARNT	cis	cerebellum	SCAN
rs12568757	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs12568757	CTSS	cis	parietal	SCAN
rs12568757	CTSS	cis	Thyroid	GTEx
rs12568757	RP11-316M1.12	cis	Thyroid	GTEx
rs12568757	ARNT	cis	lesional skin	skin_eQTL
rs12568757	CTSS	cis	multi-tissue	Pritchard
rs12568757	HORMAD1	cis	parietal	SCAN
rs12568757	CTSS	cis	lymphoblastoid	seeQTL
rs12568757	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs12568757	CTSK	cis	parietal	SCAN
rs12568757	MLLT11	cis	lymphoblastoid	seeQTL
rs12568757	RP11-316M1.12	cis	lung	GTEx
rs12568757	CTSS	cis	cerebellum	SCAN
rs12568757	FMO5	cis	cerebellum	SCAN
rs12568757	CTSK	cis	cerebellum	SCAN
rs12568757	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12568757	ARNT	cis	uninvolved skin	skin_eQTL
rs12568757	MCL1	cis	cerebellum	SCAN
rs12568757	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs12568757	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs12568757	HORMAD1	cis	Esophagus Mucosa	GTEx
rs12568757	RP11-316M1.12	cis	Whole Blood	GTEx
rs12568757	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs12568757	ARNT	cis	normal skin	skin_eQTL
rs12568757	CTSK	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150704000-150736600	Weak transcription	Fetal Stomach	stomach
2	chr1:150708400-150733000	Weak transcription	Fetal Intestine Large	intestine
3	chr1:150711000-150735600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:150712000-150737800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:150714800-150732200	Weak transcription	Stomach Mucosa	stomach
6	chr1:150715800-150736200	Weak transcription	Small Intestine	intestine
7	chr1:150716600-150737000	Weak transcription	Pancreas	Pancrea
8	chr1:150717000-150730800	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:150717000-150731000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr1:150717000-150731400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:150717000-150732000	Strong transcription	Primary B cells from cord blood	blood
12	chr1:150717000-150732200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr1:150717000-150732200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:150717000-150732400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:150717000-150732800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:150717000-150733000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:150717200-150730600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:150717200-150730800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:150717200-150731000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:150717200-150733600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:150717400-150730600	Strong transcription	Primary T cells from cord blood	blood
22	chr1:150717400-150731400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:150720200-150736200	Weak transcription	Colonic Mucosa	Colon
24	chr1:150720600-150737800	Weak transcription	Brain Substantia Nigra	brain
25	chr1:150722400-150737000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:150722600-150730600	Strong transcription	Liver	Liver
27	chr1:150723000-150738000	Weak transcription	Right Ventricle	heart
28	chr1:150723200-150729800	Strong transcription	Spleen	Spleen
29	chr1:150724200-150733200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:150724400-150730200	Strong transcription	GM12878-XiMat	blood
31	chr1:150724400-150730800	Strong transcription	Primary hematopoietic stem cells	blood
32	chr1:150724400-150737800	Weak transcription	Aorta	Aorta
33	chr1:150724600-150730400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:150724600-150736200	Weak transcription	Gastric	stomach
35	chr1:150724600-150736400	Weak transcription	Esophagus	oesophagus
36	chr1:150724800-150733000	Weak transcription	Fetal Intestine Small	intestine
37	chr1:150725800-150731400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:150726200-150730800	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:150726200-150730800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:150726400-150730800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:150727800-150732400	Weak transcription	Left Ventricle	heart
42	chr1:150727800-150734600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:150727800-150736200	Weak transcription	Adipose Nuclei	Adipose
44	chr1:150727800-150736200	Weak transcription	Lung	lung
45	chr1:150727800-150736400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:150727800-150737000	Weak transcription	Thymus	Thymus
47	chr1:150728000-150732200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:150728000-150734600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:150729000-150732200	Genic enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:150729200-150731000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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