Variant report

Variant	rs1764347
Chromosome Location	chr1:225699916-225699917
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	chr1:225698646..225701113-chr1:225965307..225966901,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10799310	0.83[EUR][1000 genomes]
rs12071529	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1222434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1222439	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1336480	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1360958	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1629896	0.88[TSI][hapmap]
rs1764345	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771318	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890999	0.88[EUR][1000 genomes]
rs1891000	0.82[AMR][1000 genomes]
rs2035916	0.87[EUR][1000 genomes]
rs3904084	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs4233220	0.83[EUR][1000 genomes]
rs4554690	0.82[EUR][1000 genomes]
rs475794	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs481746	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs499385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs516323	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs525062	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs526221	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs544404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs566085	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59363938	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6426075	0.89[TSI][hapmap]
rs6692054	0.83[EUR][1000 genomes]
rs72750896	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7545317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs954534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9651009	0.82[EUR][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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2756886	chr1:225665694-225703485	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv2759003	chr1:225665694-225703485	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv4720	chr1:225673218-225718009	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1764347	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225677200-225703600	Weak transcription	Fetal Brain Female	brain
2	chr1:225687000-225705000	Weak transcription	Spleen	Spleen
3	chr1:225687400-225704400	Weak transcription	Fetal Stomach	stomach
4	chr1:225688600-225704600	Weak transcription	Placenta	Placenta
5	chr1:225688800-225711400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:225689200-225721000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:225691000-225706200	Weak transcription	Primary B cells from cord blood	blood
8	chr1:225691200-225705000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:225692600-225704800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:225693200-225702800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:225695400-225704800	Weak transcription	Fetal Brain Male	brain
12	chr1:225695600-225721200	Weak transcription	Fetal Kidney	kidney
13	chr1:225696600-225701800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:225696600-225705000	Weak transcription	Gastric	stomach
15	chr1:225696800-225704800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:225697000-225701200	Strong transcription	Fetal Lung	lung
17	chr1:225697000-225701200	Weak transcription	HepG2	liver
18	chr1:225697200-225701400	Weak transcription	Fetal Intestine Small	intestine
19	chr1:225697200-225703400	Weak transcription	Ovary	ovary
20	chr1:225697200-225704800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:225697200-225704800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:225697200-225704800	Weak transcription	Pancreas	Pancrea
23	chr1:225697200-225705000	Weak transcription	Esophagus	oesophagus
24	chr1:225697200-225705000	Weak transcription	Lung	lung
25	chr1:225697200-225705400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:225697200-225711200	Weak transcription	Fetal Heart	heart
27	chr1:225697200-225716600	Weak transcription	Right Atrium	heart
28	chr1:225697400-225700000	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:225697400-225701400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:225697400-225705000	Weak transcription	Aorta	Aorta
31	chr1:225697400-225705000	Weak transcription	Right Ventricle	heart
32	chr1:225697400-225715400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:225697400-225722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:225697600-225702200	Weak transcription	Stomach Mucosa	stomach
35	chr1:225697600-225703400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:225697600-225703800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:225697800-225701600	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:225697800-225701600	Strong transcription	HSMM	muscle
39	chr1:225697800-225702200	Strong transcription	Osteobl	bone
40	chr1:225697800-225703000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:225697800-225703400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:225697800-225703400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:225697800-225703400	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:225697800-225703800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:225697800-225704800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:225697800-225705400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:225697800-225705400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:225697800-225706200	Weak transcription	Psoas Muscle	Psoas
49	chr1:225697800-225706800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:225697800-225707800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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