Variant report

Variant	rs6852735
Chromosome Location	chr4:15596453-15596454
allele	A/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	chr4:15595283-15596464	K562	blood:	n/a	n/a
2	POLR2A	chr4:15595942-15596458	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:15596103-15596565	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15589260..15592249-chr4:15595653..15597303,2	K562	blood:

Variant related genes	Relation type
CC2D2A	TF binding region
ENSG00000048342	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10001565	1.00[CHB][hapmap]
rs10005305	0.84[AFR][1000 genomes]
rs10008878	0.86[AFR][1000 genomes]
rs10009089	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015827	0.81[ASN][1000 genomes]
rs10017222	0.81[ASN][1000 genomes]
rs10025875	0.86[AFR][1000 genomes]
rs10034315	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433813	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11722757	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723478	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726647	0.93[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11732953	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12642407	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646913	1.00[CHB][hapmap]
rs12650529	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106528	0.85[JPT][hapmap]
rs13131119	0.85[JPT][hapmap]
rs13134177	0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13144428	0.85[JPT][hapmap]
rs13150957	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1468735	0.85[JPT][hapmap]
rs16892135	0.85[JPT][hapmap]
rs16892143	0.85[JPT][hapmap]
rs17406128	1.00[CHB][hapmap]
rs17476670	0.85[JPT][hapmap]
rs1786	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041672	0.85[JPT][hapmap]
rs2041673	0.85[JPT][hapmap]
rs28394730	0.87[AFR][1000 genomes]
rs28402170	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28447067	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28644177	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28820655	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34473224	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34559117	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34831330	0.85[JPT][hapmap]
rs34955342	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35013326	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35120298	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756247	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3775956	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3775957	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41417147	0.85[JPT][hapmap]
rs4257653	0.96[ASN][1000 genomes]
rs4267734	0.85[JPT][hapmap]
rs4301111	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4326008	0.85[JPT][hapmap]
rs4331772	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346644	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4396986	0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4423870	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484296	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4549375	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4554069	0.87[AFR][1000 genomes]
rs4600905	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698116	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414764	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449150	0.85[JPT][hapmap];0.82[AFR][1000 genomes]
rs6449152	0.81[ASN][1000 genomes]
rs6815254	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6816982	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6823775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824422	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825051	0.85[JPT][hapmap];0.83[AFR][1000 genomes]
rs6825815	0.85[JPT][hapmap]
rs6826058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827406	0.81[ASN][1000 genomes]
rs6828776	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835038	0.85[JPT][hapmap]
rs6839654	0.86[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6843740	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6844141	0.85[JPT][hapmap]
rs6848779	0.86[AFR][1000 genomes]
rs6857442	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667175	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7672311	1.00[CHB][hapmap]
rs7698596	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9994518	0.87[AFR][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6852735	LOC285550	cis	uninvolved skin	skin_eQTL
rs6852735	LOC285550	cis	normal skin	skin_eQTL
rs6852735	LOC285550	cis	lesional skin	skin_eQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
2	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
3	chr4:15554600-15601400	Weak transcription	A549	lung
4	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
5	chr4:15564000-15600600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:15564400-15603200	Weak transcription	HMEC	breast
7	chr4:15564600-15603600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
9	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
10	chr4:15565600-15604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:15565600-15611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:15565800-15605000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:15566200-15596800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:15568400-15655600	Weak transcription	Gastric	stomach
15	chr4:15569600-15603600	Weak transcription	Spleen	Spleen
16	chr4:15569600-15604200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:15570200-15601800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:15570600-15602000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:15570600-15602000	Weak transcription	Pancreas	Pancrea
20	chr4:15571000-15597200	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:15572200-15601200	Weak transcription	NHLF	lung
22	chr4:15572200-15601800	Weak transcription	Brain Angular Gyrus	brain
23	chr4:15572200-15601800	Weak transcription	NHEK	skin
24	chr4:15572200-15604000	Weak transcription	Primary T cells from cord blood	blood
25	chr4:15572200-15604200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:15573200-15603800	Weak transcription	Fetal Intestine Small	intestine
27	chr4:15575200-15618000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:15577800-15599000	Weak transcription	Left Ventricle	heart
29	chr4:15577800-15602800	Weak transcription	Placenta	Placenta
30	chr4:15578000-15599000	Weak transcription	Aorta	Aorta
31	chr4:15579000-15599200	Weak transcription	Osteobl	bone
32	chr4:15579200-15598600	Weak transcription	Liver	Liver
33	chr4:15580400-15600000	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:15583400-15599200	Weak transcription	NH-A	brain
35	chr4:15583800-15596600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:15586400-15599000	Weak transcription	Brain Anterior Caudate	brain
37	chr4:15587200-15612600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:15588200-15601200	Weak transcription	Primary B cells from cord blood	blood
39	chr4:15589000-15600000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:15589200-15602800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:15589600-15602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:15589600-15603000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:15589800-15599000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:15589800-15621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:15590000-15596800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:15590000-15603200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:15590000-15615600	Weak transcription	Lung	lung
48	chr4:15590200-15597200	Weak transcription	Fetal Lung	lung
49	chr4:15590200-15598600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:15590400-15604200	Weak transcription	Fetal Intestine Large	intestine

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