Variant report

Variant	rs4077168
Chromosome Location	chr1:153775017-153775018
allele	A/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	chr1:153774428..153778178-chr1:153892159..153894443,3	MCF-7	breast:
2	chr1:153767398..153773135-chr1:153773279..153780360,13	K562	blood:
3	chr1:153763846..153765824-chr1:153774129..153777112,2	MCF-7	breast:
4	chr1:153774020..153776363-chr1:153779136..153780973,3	K562	blood:
5	chr1:153766759..153769064-chr1:153773513..153776201,3	K562	blood:
6	chr1:153769239..153773675-chr1:153774397..153779052,9	K562	blood:
7	chr1:153754359..153756426-chr1:153773567..153776209,2	MCF-7	breast:
8	chr1:153769854..153772514-chr1:153774618..153776414,2	MCF-7	breast:
9	chr1:153641134..153643964-chr1:153774101..153775985,2	K562	blood:
10	chr1:153774195..153775832-chr1:153945042..153947231,2	MCF-7	breast:
11	chr1:153774458..153777445-chr1:153916897..153919240,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231827	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000143621	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10127983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs10752613	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10796956	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796968	0.82[AFR][1000 genomes]
rs10908557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10908558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1110165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11264532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264559	0.83[AFR][1000 genomes]
rs11264680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11264743	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11577942	0.85[AFR][1000 genomes]
rs11581644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11583152	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11583896	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11585416	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11587151	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11589857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11590099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11591134	0.81[AFR][1000 genomes]
rs12022158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12022730	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12028398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12032914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12033835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12038577	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12041850	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12041920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12042562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12042989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12043350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12401565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12403956	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12406003	0.82[AFR][1000 genomes]
rs12409811	0.85[AFR][1000 genomes]
rs12564669	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs12567313	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1572788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs34805562	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3748848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3748849	0.82[AFR][1000 genomes]
rs3791187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4363451	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4391701	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4508047	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4520447	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4595397	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4612664	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4845357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845358	0.82[AFR][1000 genomes]
rs4845576	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4845578	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs59308681	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59340135	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59678326	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6671132	0.82[AFR][1000 genomes]
rs6680140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6694061	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6700451	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6701341	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs72694220	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72694231	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72694234	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7512766	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7537691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7552274	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs946682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9660089	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4077168	CRTC2	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153757000-153779200	Weak transcription	Dnd41	blood
2	chr1:153762400-153776600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:153762600-153777600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:153762600-153777600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:153762600-153779600	Weak transcription	Gastric	stomach
6	chr1:153762600-153779600	Weak transcription	Pancreas	Pancrea
7	chr1:153763600-153776800	Weak transcription	Right Atrium	heart
8	chr1:153763600-153777800	Weak transcription	Fetal Intestine Large	intestine
9	chr1:153763600-153780000	Weak transcription	Aorta	Aorta
10	chr1:153763600-153780000	Weak transcription	Ovary	ovary
11	chr1:153763600-153780800	Weak transcription	Colonic Mucosa	Colon
12	chr1:153763800-153779400	Weak transcription	Brain Substantia Nigra	brain
13	chr1:153764000-153777000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:153764000-153777800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:153764000-153779600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:153764400-153776000	Weak transcription	HSMMtube	muscle
17	chr1:153764400-153777600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:153764400-153777600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:153764400-153778200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:153764400-153779600	Weak transcription	Brain Anterior Caudate	brain
21	chr1:153764600-153776000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:153764600-153777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:153764600-153777800	Weak transcription	NHLF	lung
24	chr1:153764800-153776000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:153764800-153776200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:153765000-153775600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:153767000-153779400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:153767600-153782600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:153767800-153779600	Weak transcription	Fetal Lung	lung
30	chr1:153768000-153775200	Weak transcription	Adipose Nuclei	Adipose
31	chr1:153768000-153777600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:153768000-153777800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:153768000-153779600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:153768000-153779600	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:153768000-153781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:153768200-153777800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:153768200-153779200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:153768200-153779400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:153768200-153779600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:153768200-153779600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:153768400-153779200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:153768400-153779800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:153768800-153779000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:153769000-153776600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:153769800-153776200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:153769800-153777000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:153769800-153777600	Weak transcription	Hela-S3	cervix
48	chr1:153769800-153777600	Weak transcription	NHEK	skin
49	chr1:153769800-153778000	Weak transcription	A549	lung
50	chr1:153769800-153779400	Weak transcription	Colon Smooth Muscle	Colon

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