Variant report

Variant	rs4771685
Chromosome Location	chr13:111168951-111168952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111160457..111163590-chr13:111168306..111171101,4	K562	blood:
2	chr13:111161146..111163590-chr13:111168306..111171101,3	K562	blood:

Variant related genes	Relation type
ENSG00000232814	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1049931	0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1049977	0.85[ASW][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1318376	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2077290	0.81[JPT][hapmap]
rs7328347	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7711	0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9559834	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats 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	16 gene(s)	inside rSNPs	diseases
6	nsv901009	chr13:111134780-111176393	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
8	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
9	nsv984479	chr13:111157297-111176429	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a
10	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4771685	COL4A2	cis	uninvolved skin	skin_eQTL
rs4771685	RAB20	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111153400-111172800	Weak transcription	Brain Substantia Nigra	brain
2	chr13:111155200-111175600	Weak transcription	Fetal Thymus	thymus
3	chr13:111159600-111172200	Weak transcription	Brain Hippocampus Middle	brain
4	chr13:111159600-111176800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:111160000-111172800	Weak transcription	Brain Anterior Caudate	brain
6	chr13:111160800-111172200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:111160800-111172600	Weak transcription	Esophagus	oesophagus
8	chr13:111160800-111176400	Weak transcription	Psoas Muscle	Psoas
9	chr13:111160800-111209600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr13:111161200-111173000	Weak transcription	Brain Germinal Matrix	brain
11	chr13:111162400-111173000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:111162600-111169800	Weak transcription	NHDF-Ad	bronchial
13	chr13:111162600-111177200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:111163000-111172200	Weak transcription	HepG2	liver
15	chr13:111163200-111169000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:111163200-111169600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:111163200-111171400	Weak transcription	Fetal Brain Male	brain
18	chr13:111163200-111175400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr13:111163400-111169800	Weak transcription	Stomach Mucosa	stomach
20	chr13:111163400-111173000	Weak transcription	Right Atrium	heart
21	chr13:111163600-111169600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr13:111164400-111170200	Weak transcription	K562	blood
23	chr13:111165000-111170600	Weak transcription	Colonic Mucosa	Colon
24	chr13:111165200-111173200	Weak transcription	Fetal Brain Female	brain
25	chr13:111165400-111170200	Weak transcription	A549	lung
26	chr13:111165400-111170600	Weak transcription	Small Intestine	intestine
27	chr13:111165400-111173400	Weak transcription	Brain Angular Gyrus	brain
28	chr13:111165400-111179800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr13:111165600-111169200	Weak transcription	NHLF	lung
30	chr13:111165600-111170600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr13:111165600-111171000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr13:111165600-111171200	Weak transcription	NHEK	skin
33	chr13:111165600-111172800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr13:111165600-111172800	Weak transcription	HSMMtube	muscle
35	chr13:111165600-111173000	Weak transcription	Colon Smooth Muscle	Colon
36	chr13:111165600-111175600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr13:111165600-111176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr13:111165600-111176600	Weak transcription	HMEC	breast
39	chr13:111165800-111179400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr13:111166400-111170000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr13:111166600-111170600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr13:111166600-111172800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:111166600-111176800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr13:111166800-111169600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:111166800-111169800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr13:111166800-111170200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr13:111166800-111170200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:111166800-111171200	Weak transcription	Liver	Liver
49	chr13:111166800-111171600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr13:111166800-111175600	Weak transcription	H1 Cell Line	embryonic stem cell

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