Variant report

Variant	rs4666401
Chromosome Location	chr2:20673094-20673095
allele	A/G
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20672482..20676692-chr2:20708404..20712337,6	MCF-7	breast:
2	chr2:20672376..20674639-chr2:20775107..20777593,2	MCF-7	breast:
3	chr2:20671558..20673879-chr2:20833720..20836195,3	MCF-7	breast:
4	chr2:20672944..20676325-chr2:20833428..20835504,3	MCF-7	breast:
5	chr2:20671493..20673943-chr2:20675690..20678137,2	K562	blood:
6	chr2:20671299..20674236-chr2:20698430..20700653,2	MCF-7	breast:
7	chr2:20672997..20675403-chr2:20825825..20827538,2	MCF-7	breast:
8	chr2:20671643..20674525-chr2:20712663..20715414,2	MCF-7	breast:
9	chr2:20672628..20675309-chr2:20724224..20726523,3	MCF-7	breast:
10	chr2:20672268..20676296-chr2:20688942..20691347,3	MCF-7	breast:
11	chr2:20642734..20659399-chr2:20663729..20679011,83	MCF-7	breast:
12	chr2:20671303..20674787-chr2:20817796..20820495,3	MCF-7	breast:
13	chr2:20673030..20677020-chr2:20693011..20697499,5	MCF-7	breast:
14	chr2:20643286..20659825-chr2:20662702..20680153,143	MCF-7	breast:
15	chr2:20670475..20680240-chr2:20690452..20700902,27	MCF-7	breast:
16	chr2:20672359..20675395-chr2:20791588..20794209,4	MCF-7	breast:
17	chr12:56222330..56225144-chr2:20671588..20674232,2	MCF-7	breast:
18	chr2:20645693..20649420-chr2:20672488..20676639,4	K562	blood:
19	chr2:20645693..20649020-chr2:20672488..20676070,5	K562	blood:
20	chr2:20670492..20674142-chr2:20847905..20851318,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1002162	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs10191983	0.81[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10205221	0.81[CEU][hapmap]
rs10856799	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11675571	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11898154	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11901246	0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12478968	0.82[EUR][1000 genomes]
rs12988451	0.81[CEU][hapmap]
rs12997261	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs13016649	1.00[ASW][hapmap]
rs13021908	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1453051	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs168195	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1872070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084919	0.85[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2348707	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs342057	0.82[CEU][hapmap]
rs342107	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs342110	0.92[CEU][hapmap]
rs342114	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs342116	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs342118	0.81[CEU][hapmap]
rs342124	0.83[GIH][hapmap];0.81[MEX][hapmap]
rs4666308	0.82[CEU][hapmap]
rs4666398	0.83[EUR][1000 genomes]
rs4666402	0.81[CEU][hapmap]
rs4666407	0.81[AMR][1000 genomes]
rs4666408	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4666409	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6531240	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6704834	0.81[CEU][hapmap]
rs715670	0.81[CEU][hapmap]
rs7601359	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs959058	0.82[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs9917322	0.81[CEU][hapmap]

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	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv873722	chr2:20652507-20705910	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4666401	HS1BP3	cis	parietal	SCAN
rs4666401	FAM49A	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20653400-20674000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:20666400-20681800	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:20667600-20673800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:20667600-20674000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:20667800-20673800	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:20668000-20674000	Weak transcription	Ovary	ovary
7	chr2:20668200-20674000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:20669800-20673800	Weak transcription	Pancreas	Pancrea
9	chr2:20669800-20674800	Weak transcription	Stomach Mucosa	stomach
10	chr2:20670800-20673800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:20670800-20673800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:20671400-20676000	Enhancers	Liver	Liver
13	chr2:20671600-20675600	Enhancers	Placenta	Placenta
14	chr2:20671800-20673400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr2:20671800-20675000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:20671800-20675400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:20672000-20673200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:20672000-20673200	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr2:20672000-20673200	Enhancers	Gastric	stomach
20	chr2:20672000-20673200	Enhancers	Psoas Muscle	Psoas
21	chr2:20672000-20674200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr2:20672000-20675200	Enhancers	Brain Anterior Caudate	brain
23	chr2:20672000-20681800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:20672200-20674400	Weak transcription	HSMMtube	muscle
25	chr2:20672200-20675400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:20672400-20673200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:20672400-20673400	Enhancers	Esophagus	oesophagus
28	chr2:20672400-20674200	Enhancers	Left Ventricle	heart
29	chr2:20672400-20675000	Enhancers	Fetal Muscle Trunk	muscle
30	chr2:20672400-20675000	Enhancers	Right Atrium	heart
31	chr2:20672400-20675600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:20672400-20675600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:20672600-20674000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:20672800-20673800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:20673000-20673200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:20673000-20674000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:20673000-20674000	Weak transcription	Brain Substantia Nigra	brain
38	chr2:20673000-20674000	Enhancers	HepG2	liver
39	chr2:20673000-20675000	Enhancers	Brain Cingulate Gyrus	brain
40	chr2:20673000-20675800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr2:20673000-20687000	Weak transcription	Spleen	Spleen

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