Variant report

Variant	rs4612664
Chromosome Location	chr1:153822673-153822674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153821048..153823410-chr1:153958136..153960515,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143545	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10127983	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1043608	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10559	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10796956	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10796968	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10908557	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10908558	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10908627	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1110165	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264532	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264559	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264567	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264619	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264620	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264680	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264734	0.80[EUR][1000 genomes]
rs11264743	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs11264763	0.81[ASN][1000 genomes]
rs11264866	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264871	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264873	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264875	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264886	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11577942	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11581644	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11583152	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583896	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11585416	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11586075	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11586593	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11586830	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11587151	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11589043	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11589857	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11590099	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11591134	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12022158	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12022730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12023699	0.82[ASN][1000 genomes]
rs12027783	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12028398	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12032914	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12033835	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12038577	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041850	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12041920	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12042562	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12042989	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12043350	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12048137	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12401565	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12403956	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12406003	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12409811	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12564669	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs12567313	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1572788	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34805562	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3748848	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3748849	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3791187	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4077168	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4363451	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4391701	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4508047	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4520447	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4595397	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845357	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845358	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845576	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845578	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845583	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845585	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58095661	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59308681	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59340135	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59678326	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60150125	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61219911	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6427329	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6659220	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6666703	0.81[ASN][1000 genomes]
rs6671132	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6672856	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6680140	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6694061	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6700451	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6701341	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6724	0.84[ASN][1000 genomes]
rs72694220	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72694231	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72694234	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512766	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7521303	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7537691	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7552274	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552737	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs8450	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs946682	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9660089	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
7	esv1825076	chr1:153779296-153843413	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4612664	CRTC2	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153781600-153826800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:153791800-153845600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:153800000-153824400	Weak transcription	Brain Germinal Matrix	brain
4	chr1:153800600-153824600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:153800800-153823600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:153800800-153823800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:153800800-153824200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:153800800-153824400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:153800800-153824400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:153800800-153824400	Weak transcription	Fetal Intestine Large	intestine
11	chr1:153800800-153824800	Weak transcription	Fetal Lung	lung
12	chr1:153800800-153825000	Weak transcription	HSMM	muscle
13	chr1:153800800-153825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:153800800-153825400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:153800800-153825400	Weak transcription	Pancreas	Pancrea
16	chr1:153800800-153827000	Weak transcription	HUVEC	blood vessel
17	chr1:153800800-153830800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:153800800-153832600	Weak transcription	Aorta	Aorta
19	chr1:153800800-153832800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:153800800-153835600	Weak transcription	Ovary	ovary
21	chr1:153800800-153850800	Weak transcription	A549	lung
22	chr1:153800800-153852800	Weak transcription	Fetal Brain Female	brain
23	chr1:153800800-153852800	Weak transcription	Placenta	Placenta
24	chr1:153800800-153852800	Weak transcription	Left Ventricle	heart
25	chr1:153800800-153853000	Weak transcription	Fetal Kidney	kidney
26	chr1:153801000-153823600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:153801000-153823600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:153801000-153824200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:153801000-153824400	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:153801000-153824600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:153801200-153823200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:153801200-153824400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:153801200-153824600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:153801200-153829800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:153801200-153829800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:153801400-153823400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:153801400-153823400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:153801600-153824600	Weak transcription	NHEK	skin
39	chr1:153801600-153845800	Weak transcription	Lung	lung
40	chr1:153801800-153823800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:153801800-153836600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:153803800-153824800	Weak transcription	Hela-S3	cervix
43	chr1:153806000-153827400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:153806200-153845400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:153807600-153824600	Weak transcription	Thymus	Thymus
46	chr1:153808000-153823800	Weak transcription	Dnd41	blood
47	chr1:153811600-153823000	Weak transcription	Fetal Stomach	stomach
48	chr1:153814600-153823200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:153814600-153824600	Weak transcription	Spleen	Spleen
50	chr1:153814600-153827400	Weak transcription	Colonic Mucosa	Colon

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