Variant report

Variant	rs1971378
Chromosome Location	chr1:150597261-150597262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150595731..150598614-chr1:150617206..150619225,2	K562	blood:
2	chr1:150548506..150553393-chr1:150590797..150599175,18	MCF-7	breast:
3	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
4	chr1:150532182..150537720-chr1:150588719..150604935,28	MCF-7	breast:
5	chr1:150595731..150598614-chr1:150616127..150619225,3	K562	blood:
6	chr1:150596818..150598421-chr1:150785582..150787541,2	MCF-7	breast:
7	chr1:150531290..150540028-chr1:150591374..150603951,29	MCF-7	breast:
8	chr1:150548467..150555490-chr1:150590800..150598161,17	MCF-7	breast:
9	chr1:150544073..150554289-chr1:150582699..150598712,61	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264584	Chromatin interaction
ENSG00000264508	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1053732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888384	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888385	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204668	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11204669	0.80[ASN][1000 genomes]
rs11204675	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204677	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204678	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204679	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204680	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204693	0.84[CHD][hapmap];0.86[YRI][hapmap]
rs11204695	0.82[CHD][hapmap];0.80[GIH][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap]
rs11585169	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12116492	0.89[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap]
rs12125672	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12126271	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12139563	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12406712	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12568757	0.82[CHD][hapmap];0.86[YRI][hapmap]
rs12746899	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2048558	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3738484	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738485	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3754209	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970918	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970923	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970924	0.82[CHD][hapmap];0.80[GIH][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs4970926	0.82[CHD][hapmap];0.80[GIH][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs4971041	0.82[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs55862611	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61820165	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6669122	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694531	0.82[CHD][hapmap];0.80[GIH][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap]
rs6697620	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6698495	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7520022	0.81[CHD][hapmap];0.86[YRI][hapmap]
rs878471	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs9733	0.83[MKK][hapmap];0.86[YRI][hapmap]
rs9803935	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs1971378	CTSK	cis	multi-tissue	Pritchard
rs1971378	CTSS	cis	parietal	SCAN
rs1971378	POLR3GL	cis	cerebellum	SCAN
rs1971378	GOLPH3L	cis	Nerve Tibial	GTEx
rs1971378	ARNT	cis	Thyroid	GTEx
rs1971378	HORMAD1	cis	Esophagus Mucosa	GTEx
rs1971378	ARNT	cis	parietal	SCAN
rs1971378	TXNIP	cis	parietal	SCAN
rs1971378	CTSS	cis	Nerve Tibial	GTEx
rs1971378	MCL1	cis	cerebellum	SCAN
rs1971378	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs1971378	TCHHL1	cis	parietal	SCAN
rs1971378	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs1971378	PSMD4	cis	parietal	SCAN
rs1971378	CTSS	cis	multi-tissue	Pritchard
rs1971378	CTSK	cis	parietal	SCAN
rs1971378	CTSS	cis	cerebellum	SCAN
rs1971378	CTSK	cis	lymphoblastoid	seeQTL
rs1971378	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs1971378	HORMAD1	cis	Nerve Tibial	GTEx
rs1971378	CTSS	cis	lymphoblastoid	seeQTL
rs1971378	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs1971378	CTSK	cis	cerebellum	SCAN
rs1971378	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs1971378	ARNT	cis	cerebellum	SCAN
rs1971378	FMO5	cis	cerebellum	SCAN
rs1971378	HORMAD1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150584400-150600600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:150584800-150600200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:150585000-150600000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:150585200-150600200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:150586600-150600400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr1:150587800-150598800	Strong transcription	Dnd41	blood
7	chr1:150587800-150600000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:150587800-150600400	Strong transcription	Brain Germinal Matrix	brain
9	chr1:150588200-150600200	Strong transcription	Fetal Intestine Large	intestine
10	chr1:150588600-150601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:150591400-150599800	Strong transcription	Fetal Brain Female	brain
12	chr1:150591600-150599800	Strong transcription	Fetal Lung	lung
13	chr1:150591600-150600000	Strong transcription	Thymus	Thymus
14	chr1:150591800-150600600	Genic enhancers	HMEC	breast
15	chr1:150592000-150599600	Strong transcription	Fetal Kidney	kidney
16	chr1:150592200-150599000	Genic enhancers	K562	blood
17	chr1:150592600-150600400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:150592800-150600200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:150592800-150600200	Strong transcription	Fetal Intestine Small	intestine
20	chr1:150593000-150599400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:150593000-150600200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:150593000-150600600	Strong transcription	Fetal Stomach	stomach
23	chr1:150593200-150600000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:150593200-150600400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:150593400-150600400	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:150593600-150600200	Strong transcription	Osteobl	bone
27	chr1:150594200-150597600	Genic enhancers	Placenta	Placenta
28	chr1:150594200-150598200	Strong transcription	Brain Hippocampus Middle	brain
29	chr1:150594200-150599800	Strong transcription	HSMMtube	muscle
30	chr1:150594200-150600000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:150594200-150600000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:150594200-150600200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:150594200-150600200	Strong transcription	Colon Smooth Muscle	Colon
34	chr1:150594200-150600400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:150594200-150600600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:150594400-150598000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:150594400-150598600	Strong transcription	Aorta	Aorta
38	chr1:150594400-150599000	Strong transcription	Fetal Brain Male	brain
39	chr1:150594400-150599800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:150594400-150600000	Strong transcription	Colonic Mucosa	Colon
41	chr1:150594400-150600200	Strong transcription	NH-A	brain
42	chr1:150594600-150600000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:150594600-150600200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:150594600-150600200	Strong transcription	HSMM	muscle
45	chr1:150594800-150599600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:150594800-150599800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:150594800-150600000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:150594800-150600000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:150594800-150600200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:150595000-150598400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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