Variant report

Variant	rs11204735
Chromosome Location	chr1:150841667-150841668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150841045..150846072-chr1:150846132..150851412,6	MCF-7	breast:
2	chr1:150551554..150554237-chr1:150841664..150843892,2	K562	blood:
3	chr1:150835101..150837976-chr1:150840921..150842454,2	K562	blood:
4	chr1:150834498..150838027-chr1:150838214..150842454,5	K562	blood:

Variant related genes	Relation type
ENSG00000143437	Chromatin interaction
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 24 )

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

rs_ID	r²[population]
rs1081512	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11204693	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11204695	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11204725	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs11204737	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	0.83[EUR][1000 genomes]
rs11587718	0.84[YRI][hapmap]
rs12125650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12126004	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12402006	0.95[EUR][1000 genomes]
rs12404199	0.95[EUR][1000 genomes]
rs12410050	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12568757	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs12725806	0.82[ASN][1000 genomes]
rs12758227	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1673160	0.84[YRI][hapmap]
rs1722784	0.91[YRI][hapmap]
rs17599629	0.83[YRI][hapmap]
rs2039590	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2089081	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs267733	0.83[YRI][hapmap]
rs34002273	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3754211	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs486836	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4970926	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4970932	0.88[EUR][1000 genomes]
rs4970976	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587551	0.81[EUR][1000 genomes]
rs6694531	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7412746	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7520022	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7534124	0.84[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	nsv1010875	chr1:150796816-150845827	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs11204735	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11204735	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204735	HORMAD1	cis	Nerve Tibial	GTEx
rs11204735	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs11204735	ARNT	cis	multi-tissue	Pritchard
rs11204735	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11204735	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11204735	CTSK	cis	multi-tissue	Pritchard
rs11204735	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11204735	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11204735	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11204735	HORMAD1	cis	uninvolved skin	skin_eQTL
rs11204735	RP11-316M1.12	cis	lung	GTEx
rs11204735	HORMAD1	cis	lesional skin	skin_eQTL
rs11204735	CTSS	cis	Thyroid	GTEx
rs11204735	RP11-316M1.12	cis	Artery Tibial	GTEx
rs11204735	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs11204735	ARNT	cis	uninvolved skin	skin_eQTL
rs11204735	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11204735	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs11204735	RP11-316M1.12	cis	Whole Blood	GTEx
rs11204735	RP11-316M1.12	cis	Thyroid	GTEx
rs11204735	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs11204735	ARNT	cis	normal skin	skin_eQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150807400-150847000	Weak transcription	Colonic Mucosa	Colon
2	chr1:150808800-150847000	Weak transcription	Psoas Muscle	Psoas
3	chr1:150809200-150846800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:150809600-150846000	Weak transcription	Pancreas	Pancrea
5	chr1:150810400-150846600	Weak transcription	Fetal Heart	heart
6	chr1:150812000-150847000	Weak transcription	Gastric	stomach
7	chr1:150812400-150842000	Weak transcription	Esophagus	oesophagus
8	chr1:150812400-150846800	Weak transcription	Fetal Kidney	kidney
9	chr1:150812600-150846000	Weak transcription	Small Intestine	intestine
10	chr1:150812600-150846800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:150815400-150842400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:150815400-150846800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:150820600-150846800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:150821200-150846600	Weak transcription	Aorta	Aorta
15	chr1:150821200-150846600	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:150821200-150846800	Weak transcription	Brain Anterior Caudate	brain
17	chr1:150821200-150848600	Weak transcription	Spleen	Spleen
18	chr1:150822400-150846800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:150825000-150846600	Weak transcription	K562	blood
20	chr1:150825000-150848000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:150825200-150846600	Weak transcription	Fetal Brain Female	brain
22	chr1:150825200-150846800	Weak transcription	Brain Substantia Nigra	brain
23	chr1:150825200-150846800	Weak transcription	Fetal Brain Male	brain
24	chr1:150825400-150846000	Weak transcription	NHLF	lung
25	chr1:150825400-150846200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:150825600-150846800	Weak transcription	HSMMtube	muscle
27	chr1:150826000-150847800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:150826400-150845800	Weak transcription	HepG2	liver
29	chr1:150826600-150846800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:150827000-150848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:150827400-150846600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:150827800-150847000	Weak transcription	A549	lung
33	chr1:150828000-150847000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:150828400-150845200	Weak transcription	Fetal Intestine Large	intestine
35	chr1:150828400-150847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:150828400-150847000	Weak transcription	Brain Germinal Matrix	brain
37	chr1:150828600-150846400	Weak transcription	Dnd41	blood
38	chr1:150829400-150844200	Weak transcription	Thymus	Thymus
39	chr1:150829400-150847000	Weak transcription	Right Ventricle	heart
40	chr1:150830000-150847000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:150830400-150845800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:150830600-150842400	Weak transcription	NHDF-Ad	bronchial
43	chr1:150830800-150845000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:150830800-150845200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:150830800-150845800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:150830800-150846800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:150831000-150844200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:150831000-150844400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:150831000-150844400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:150831000-150844400	Weak transcription	HUVEC	blood vessel

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