Variant report

Variant	rs163633
Chromosome Location	chr5:77940652-77940653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:77940595-77941058	IMR90	lung:	n/a	n/a
2	RAD21	chr5:77940606-77940888	SK-N-SH_RA	brain:	n/a	n/a
3	TFAP2C	chr5:77940581-77941056	Hela-S3	cervix:	n/a	chr5:77940726-77940741
4	POLR2A	chr5:77940490-77940746	MCF10A-Er-Src	breast:	n/a	n/a
5	FOXA1	chr5:77940593-77940931	T-47D	breast:	n/a	n/a
6	FOXA1	chr5:77940581-77940839	T-47D	breast:	n/a	n/a
7	KAP1	chr5:77940646-77941026	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:77940516..77942352-chr5:77943015..77944536,2	MCF-7	breast:

Variant related genes	Relation type
LHFPL2	TF binding region
ENSG00000145685	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10060702	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs168190	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs171035	0.98[ASN][1000 genomes]
rs189322	0.93[ASN][1000 genomes]
rs341917	0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs341918	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs341919	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs341920	0.91[ASN][1000 genomes]
rs341924	0.92[ASN][1000 genomes]
rs341925	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341926	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs341927	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341928	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs341930	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs344639	0.93[ASN][1000 genomes]
rs461989	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522738	chr5:77434730-78063683	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3522739	chr5:77434730-78063683	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv949530	chr5:77830403-78477017	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv830356	chr5:77847022-78011999	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1021768	chr5:77881915-78465489	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv2762527	chr5:77921199-78548196	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv1792242	chr5:77927033-77966625	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv1841124	chr5:77937453-77944988	Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv528833	chr5:77937453-78016860	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv968954	chr5:77939197-77940805	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:77928200-77942400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:77931000-77942800	Weak transcription	K562	blood
3	chr5:77933800-77941400	Weak transcription	Right Atrium	heart
4	chr5:77933800-77943200	Weak transcription	Esophagus	oesophagus
5	chr5:77934600-77942400	Weak transcription	Colonic Mucosa	Colon
6	chr5:77935200-77942000	Weak transcription	Right Ventricle	heart
7	chr5:77935200-77942600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:77935400-77942000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:77935400-77942600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:77936000-77942600	Weak transcription	Fetal Brain Female	brain
11	chr5:77936800-77940800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:77937000-77942600	Weak transcription	Left Ventricle	heart
13	chr5:77937000-77942600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:77937000-77943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:77937000-77943200	Weak transcription	Psoas Muscle	Psoas
16	chr5:77937200-77940800	Weak transcription	NHDF-Ad	bronchial
17	chr5:77937200-77940800	Weak transcription	Osteobl	bone
18	chr5:77937200-77941200	Weak transcription	Adipose Nuclei	Adipose
19	chr5:77937200-77942000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:77937200-77942000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:77937200-77942000	Weak transcription	Fetal Heart	heart
22	chr5:77937200-77942000	Weak transcription	Small Intestine	intestine
23	chr5:77937200-77942000	Weak transcription	NHLF	lung
24	chr5:77937200-77942200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:77937200-77942400	Weak transcription	HSMM	muscle
26	chr5:77937200-77942600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:77937200-77942600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:77937200-77942600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:77937200-77942800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:77937200-77942800	Enhancers	HepG2	liver
31	chr5:77937200-77943000	Weak transcription	Brain Angular Gyrus	brain
32	chr5:77937200-77943200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:77937200-77943200	Weak transcription	Gastric	stomach
34	chr5:77937400-77942000	Weak transcription	HUVEC	blood vessel
35	chr5:77937400-77942600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:77937400-77943000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr5:77937600-77942000	Genic enhancers	A549	lung
38	chr5:77937600-77942200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:77937800-77941000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:77937800-77941800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr5:77938000-77942000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:77938600-77941800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr5:77938800-77942600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr5:77939000-77940800	Weak transcription	Fetal Lung	lung
45	chr5:77939000-77940800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:77939000-77941800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:77939000-77941800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr5:77939000-77943200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:77939000-77943200	Weak transcription	Lung	lung
50	chr5:77939000-77943200	Weak transcription	Pancreas	Pancrea

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