Variant report

Variant	rs11204749
Chromosome Location	chr1:150929563-150929564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150929533-150929629	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150927491..150931705-chr1:150932102..150935142,7	K562	blood:
2	chr1:150929171..150929726-chr1:150951821..150952601,2	MCF-7	breast:

Variant related genes	Relation type
SETDB1	TF binding region
ENSG00000143379	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10305720	0.81[EUR][1000 genomes]
rs10399947	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888391	0.87[CEU][hapmap]
rs10888394	0.86[CEU][hapmap]
rs10888395	0.82[EUR][1000 genomes]
rs10888397	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10888398	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204722	0.82[CEU][hapmap]
rs11204726	0.87[CEU][hapmap]
rs11204739	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204742	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204743	0.96[ASN][1000 genomes]
rs11204747	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204748	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204750	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11579736	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11581757	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583707	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11589886	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11800855	0.85[EUR][1000 genomes]
rs12059949	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12067685	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12075597	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12085336	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs12090215	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096831	0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12097963	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12141871	0.83[CHB][hapmap]
rs12145224	0.84[CHB][hapmap]
rs12405726	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12409208	0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12410394	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12410869	0.87[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12562939	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1546376	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16827671	0.87[CEU][hapmap]
rs1889740	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs1889741	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1972060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2004903	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124952	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228099	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2256355	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs2271076	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272214	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2280627	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2864873	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2864882	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2867296	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2867297	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34985895	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35309985	0.81[ASN][1000 genomes]
rs36008098	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3754211	0.84[YRI][hapmap]
rs3768013	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs3843843	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3849279	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4451553	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4509581	0.86[CEU][hapmap]
rs4970928	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970929	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4970930	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4970931	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4970980	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4970982	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970984	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970985	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970986	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4970987	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970988	0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59024312	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587542	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6658066	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6660845	0.80[EUR][1000 genomes]
rs6669855	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6677420	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66847267	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6686064	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72704656	0.85[EUR][1000 genomes]
rs72704679	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704682	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704685	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7514004	0.85[EUR][1000 genomes]
rs7518156	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs752376	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528773	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532045	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs7556451	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556661	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8444	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs897815	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9661876	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:29)

SNP	Gene	Cis/trans	Tissue	Source
rs11204749	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11204749	GOLPH3L	cis	Nerve Tibial	GTEx
rs11204749	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11204749	RP11-316M1.12	cis	Artery Aorta	GTEx
rs11204749	ARNT	cis	normal skin	skin_eQTL
rs11204749	RP11-316M1.12	cis	Thyroid	GTEx
rs11204749	HORMAD1	cis	normal skin	skin_eQTL
rs11204749	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11204749	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs11204749	HORMAD1	cis	uninvolved skin	skin_eQTL
rs11204749	CTSS	cis	multi-tissue	Pritchard
rs11204749	RP11-98D18.3	cis	Esophagus Mucosa	GTEx
rs11204749	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11204749	HORMAD1	cis	Nerve Tibial	GTEx
rs11204749	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs11204749	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11204749	RP11-316M1.12	cis	Artery Tibial	GTEx
rs11204749	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs11204749	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204749	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs11204749	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11204749	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs11204749	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11204749	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs11204749	HORMAD1	cis	lesional skin	skin_eQTL
rs11204749	RP11-316M1.12	cis	lung	GTEx
rs11204749	RP11-316M1.12	cis	Whole Blood	GTEx
rs11204749	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs11204749	CTSS	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150899600-150943400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:150900200-150941800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:150900400-150941000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:150900400-150942600	Weak transcription	Stomach Mucosa	stomach
5	chr1:150900400-150944200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:150901000-150941600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:150901600-150941600	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr1:150903600-150941600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:150903600-150942200	Strong transcription	Dnd41	blood
10	chr1:150903600-150942800	Strong transcription	Fetal Stomach	stomach
11	chr1:150903600-150943000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:150903600-150943200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:150903800-150942600	Strong transcription	Fetal Thymus	thymus
14	chr1:150904000-150930600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:150904400-150940800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:150904600-150942200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:150904600-150942400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:150904600-150942400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:150904600-150943400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:150904800-150936400	Strong transcription	Placenta	Placenta
21	chr1:150904800-150940800	Strong transcription	Fetal Intestine Large	intestine
22	chr1:150904800-150941800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:150904800-150941800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:150905000-150941800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:150905000-150942000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:150905000-150942400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:150905000-150943000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:150905400-150942800	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:150905600-150942000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:150906200-150942400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:150906400-150941600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:150907000-150941600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:150907000-150941800	Strong transcription	Fetal Brain Female	brain
34	chr1:150907000-150942200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:150907000-150942400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:150907200-150941600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:150908400-150941800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr1:150908600-150941600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:150908600-150941800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:150908800-150940800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:150909200-150940600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:150909400-150941800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:150909600-150941800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:150911400-150930600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:150911400-150941600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:150912000-150941600	Strong transcription	Ovary	ovary
47	chr1:150912200-150934200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:150912200-150941600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:150914200-150931200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr1:150915600-150933200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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