Variant report

Variant	rs772178
Chromosome Location	chr2:96963684-96963685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96948398..96950278-chr2:96962881..96965355,2	MCF-7	breast:
2	chr2:96857464..96859151-chr2:96962378..96965099,2	K562	blood:
3	chr2:96950791..96952713-chr2:96962295..96965071,3	MCF-7	breast:
4	chr2:96962130..96967127-chr2:96968742..96972562,9	K562	blood:
5	chr2:96953953..96959571-chr2:96963290..96968398,7	MCF-7	breast:
6	chr2:96872835..96874920-chr2:96963491..96966077,2	MCF-7	breast:
7	chr2:96961103..96962937-chr2:96963414..96964920,2	K562	blood:

Variant related genes	Relation type
ENSG00000144028	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10183151	0.95[CEU][hapmap]
rs11680950	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs1168965	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs1168966	0.86[CEU][hapmap]
rs1168968	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs1168970	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1168974	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs1168975	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs1168976	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs11693248	0.84[AMR][1000 genomes]
rs13019188	0.80[CEU][hapmap]
rs1657502	0.82[CEU][hapmap]
rs2229169	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs2301707	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2312955	0.90[CEU][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs2692894	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs2969490	0.86[CEU][hapmap]
rs2969491	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs3821051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4426564	0.90[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs4907299	0.90[CEU][hapmap];0.82[TSI][hapmap]
rs58448550	0.81[AMR][1000 genomes]
rs648225	0.87[AMR][1000 genomes]
rs749457	0.82[CEU][hapmap]
rs749459	0.82[CEU][hapmap]
rs7604842	0.95[CEU][hapmap]
rs772154	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs772175	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs810057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs893173	0.82[CEU][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs772178	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs772178	MGAT4A	cis	parietal	SCAN
rs772178	FAHD2CP	cis	Muscle Skeletal	GTEx
rs772178	GPAT2	cis	Muscle Skeletal	GTEx
rs772178	ADRA2B	cis	Thyroid	GTEx
rs772178	GPAT2	cis	Stomach	GTEx
rs772178	CIAO1	cis	lymphoblastoid	seeQTL
rs772178	ZNF514	cis	parietal	SCAN
rs772178	ADRA2B	cis	Nerve Tibial	GTEx
rs772178	MRPL30	cis	parietal	SCAN
rs772178	FAHD2CP	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96932800-96970400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:96933200-96970200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:96933200-96970400	Weak transcription	Right Atrium	heart
4	chr2:96933400-96968800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:96933400-96969000	Strong transcription	Left Ventricle	heart
6	chr2:96933400-96969200	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr2:96933400-96969400	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:96933400-96969400	Strong transcription	Brain Inferior Temporal Lobe	brain
9	chr2:96933400-96970200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:96933400-96970200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:96933400-96970200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:96933400-96970200	Strong transcription	Fetal Lung	lung
13	chr2:96933400-96970200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:96933600-96965800	Strong transcription	Lung	lung
15	chr2:96933600-96966800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:96933600-96966800	Strong transcription	Brain Germinal Matrix	brain
17	chr2:96933600-96967200	Strong transcription	Brain Angular Gyrus	brain
18	chr2:96933600-96969400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:96933600-96969400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:96933600-96969400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:96933600-96969600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:96933600-96969600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr2:96933600-96969800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:96933600-96969800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:96933600-96969800	Strong transcription	Fetal Intestine Small	intestine
26	chr2:96933600-96969800	Strong transcription	Fetal Stomach	stomach
27	chr2:96933600-96969800	Strong transcription	Hela-S3	cervix
28	chr2:96933600-96970000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:96933600-96970000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:96933600-96970000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:96933600-96970200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr2:96933600-96970200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:96933600-96970200	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:96933600-96970200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr2:96933800-96966800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:96933800-96967000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:96933800-96968000	Strong transcription	Fetal Thymus	thymus
38	chr2:96933800-96969200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:96933800-96969400	Strong transcription	Primary T cells from cord blood	blood
40	chr2:96933800-96969400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:96933800-96969400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:96933800-96969400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:96933800-96969800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:96933800-96969800	Strong transcription	Fetal Intestine Large	intestine
45	chr2:96934000-96967200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:96934200-96969400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:96934400-96966600	Strong transcription	Dnd41	blood
48	chr2:96934400-96967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:96934400-96969800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:96934600-96970000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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