Variant report

Variant	rs11204737
Chromosome Location	chr1:150847647-150847648
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150549744..150554023-chr1:150847608..150851573,5	K562	blood:
2	chr1:150847503..150849791-chr1:150897618..150900781,3	K562	blood:
3	chr1:150847223..150849804-chr14:20928193..20929999,2	MCF-7	breast:
4	chr1:150830646..150832634-chr1:150847170..150848850,2	MCF-7	breast:
5	chr1:150847356..150848927-chr1:150849575..150851202,2	K562	blood:
6	chr1:150846965..150851829-chr1:150851958..150856513,6	MCF-7	breast:
7	chr1:150549206..150551464-chr1:150847559..150850045,2	K562	blood:
8	chr1:150533798..150536086-chr1:150845330..150849365,4	MCF-7	breast:
9	chr1:150847391..150850807-chr1:150896212..150900555,5	MCF-7	breast:
10	chr1:150846616..150850276-chr1:150942456..150948926,7	MCF-7	breast:
11	chr1:150846958..150850554-chr1:150897225..150899118,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000212512	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000224800	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000165782	Chromatin interaction
ENSG00000231073	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 36 )

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

rs_ID	r²[population]
rs1081512	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11204693	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.84[TSI][hapmap]
rs11204695	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs11204725	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs11204735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1136774	0.84[EUR][1000 genomes]
rs11587718	0.83[YRI][hapmap]
rs12125650	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12126004	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12402006	0.94[EUR][1000 genomes]
rs12404199	0.94[EUR][1000 genomes]
rs12410050	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12568757	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]
rs12725806	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12758227	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673160	0.83[YRI][hapmap]
rs1722784	0.91[YRI][hapmap]
rs17599629	0.83[YRI][hapmap]
rs2039590	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2089081	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs267733	0.83[YRI][hapmap]
rs34002273	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3754211	1.00[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs486836	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4970926	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap]
rs4970932	0.88[EUR][1000 genomes]
rs4970976	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6587551	0.81[EUR][1000 genomes]
rs6694531	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs7412746	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7520022	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs7534124	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv872420	chr1:150786038-150847647	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv2810	chr1:150835173-150879869	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs11204737	PSMD4	cis	parietal	SCAN
rs11204737	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs11204737	HORMAD1	cis	parietal	SCAN
rs11204737	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11204737	CTSS	cis	parietal	SCAN
rs11204737	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11204737	RP11-316M1.12	cis	Whole Blood	GTEx
rs11204737	CTSK	cis	parietal	SCAN
rs11204737	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204737	FLG	cis	cerebellum	SCAN
rs11204737	ARNT	cis	parietal	SCAN
rs11204737	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11204737	CTSS	cis	cerebellum	SCAN
rs11204737	FMO5	cis	cerebellum	SCAN
rs11204737	CTSS	cis	lymphoblastoid	seeQTL
rs11204737	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11204737	HORMAD1	cis	Nerve Tibial	GTEx
rs11204737	ARNT	cis	normal skin	skin_eQTL
rs11204737	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs11204737	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs11204737	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11204737	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11204737	CTSK	cis	multi-tissue	Pritchard
rs11204737	RP11-316M1.12	cis	Thyroid	GTEx
rs11204737	ARNT	cis	cerebellum	SCAN
rs11204737	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11204737	HORMAD1	cis	lesional skin	skin_eQTL
rs11204737	MCL1	cis	cerebellum	SCAN
rs11204737	CTSS	cis	Thyroid	GTEx
rs11204737	ARNT	cis	uninvolved skin	skin_eQTL
rs11204737	CTSK	cis	cerebellum	SCAN
rs11204737	RP11-316M1.12	cis	Artery Tibial	GTEx
rs11204737	HORMAD1	cis	uninvolved skin	skin_eQTL
rs11204737	RP11-316M1.12	cis	lung	GTEx
rs11204737	CTSK	cis	lymphoblastoid	seeQTL
rs11204737	RP11-316M1.12	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150821200-150848600	Weak transcription	Spleen	Spleen
2	chr1:150825000-150848000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:150826000-150847800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:150827000-150848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:150831000-150848200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:150834200-150847800	Weak transcription	Fetal Thymus	thymus
7	chr1:150841200-150848200	Weak transcription	Lung	lung
8	chr1:150845200-150848000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:150845800-150848200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:150846200-150847800	Enhancers	Primary B cells from cord blood	blood
11	chr1:150846400-150847800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:150846600-150847800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:150846600-150847800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:150846600-150848000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr1:150846600-150848000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:150846600-150848000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:150846600-150848200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:150846600-150848200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:150846600-150848200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:150846600-150848400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr1:150846600-150848600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:150846600-150849200	Active TSS	Ovary	ovary
23	chr1:150846600-150850000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:150846600-150850000	Active TSS	Aorta	Aorta
25	chr1:150846600-150850000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:150846800-150847800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:150846800-150847800	Enhancers	Stomach Mucosa	stomach
28	chr1:150846800-150848000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:150846800-150848000	Enhancers	Primary B cells from peripheral blood	blood
30	chr1:150846800-150848000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:150846800-150848000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:150846800-150848000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:150846800-150848000	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr1:150846800-150848000	Flanking Active TSS	Hela-S3	cervix
35	chr1:150846800-150848200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr1:150846800-150848200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr1:150846800-150848400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr1:150846800-150848800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr1:150846800-150849200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:150846800-150849200	Active TSS	NHDF-Ad	bronchial
41	chr1:150846800-150849800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:150847000-150847800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:150847000-150847800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:150847000-150847800	Enhancers	Colonic Mucosa	Colon
45	chr1:150847000-150847800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr1:150847000-150847800	Flanking Active TSS	Fetal Kidney	kidney
47	chr1:150847000-150848200	Flanking Active TSS	HUVEC	blood vessel
48	chr1:150847000-150848400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr1:150847000-150848400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr1:150847000-150848400	Flanking Active TSS	NHEK	skin

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