Variant report

Variant	rs71175434
Chromosome Location	chr4:7874704-7874705
allele	-/C
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	TCF12	chr4:7873602-7874784	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr4:7873710-7874717	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr4:7874533-7874863	HepG2	liver:	n/a	n/a
4	GTF3C2	chr4:7873909-7874975	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr4:7873874-7874709	Hela-S3	cervix:	n/a	n/a
6	GATA3	chr4:7873657-7874708	A549	lung:	n/a	n/a

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10005650	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10024625	0.90[AMR][1000 genomes]
rs28425587	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28434072	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28498817	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28607438	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28668205	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28675899	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28735181	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28735634	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28842326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4401450	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4478172	0.84[ASN][1000 genomes]
rs4488938	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4696771	0.81[AMR][1000 genomes]
rs61081420	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61214925	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6605361	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6820041	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6839086	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6842743	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73073924	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73073939	0.81[AMR][1000 genomes]
rs73088591	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73088594	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73090508	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73090513	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73090514	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7376703	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7676488	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7691757	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7695510	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9330346	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9654093	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7865400-7875800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:7866000-7875200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:7866000-7875400	Weak transcription	Stomach Mucosa	stomach
5	chr4:7866000-7877600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:7866000-7877800	Weak transcription	HepG2	liver
7	chr4:7866000-7882400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:7866000-7885600	Weak transcription	Esophagus	oesophagus
9	chr4:7869200-7880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:7869600-7877600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:7869800-7878000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:7870400-7876800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:7870400-7879200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:7870400-7882400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:7870600-7877200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:7870600-7877200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:7870600-7877600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:7870600-7878000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:7870600-7878000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:7873000-7875800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:7873200-7875200	Weak transcription	Colonic Mucosa	Colon
22	chr4:7873400-7874800	Enhancers	Adipose Nuclei	Adipose
23	chr4:7873400-7875400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:7873400-7875400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:7873400-7875600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:7873400-7875800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:7873400-7876000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:7873400-7877200	Weak transcription	Primary T cells from cord blood	blood
29	chr4:7873400-7878800	Weak transcription	Fetal Intestine Small	intestine
30	chr4:7873400-7879000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:7873400-7880000	Weak transcription	Lung	lung
32	chr4:7873400-7883000	Weak transcription	Right Ventricle	heart
33	chr4:7873600-7878000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:7873600-7878200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr4:7873800-7874800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr4:7873800-7874800	Enhancers	Colon Smooth Muscle	Colon
38	chr4:7873800-7875400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:7873800-7875600	Enhancers	NHEK	skin
40	chr4:7873800-7878200	Weak transcription	Fetal Intestine Large	intestine
41	chr4:7874000-7876000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:7874200-7874800	Enhancers	Fetal Muscle Leg	muscle
43	chr4:7874200-7875000	Enhancers	Fetal Muscle Trunk	muscle
44	chr4:7874200-7877800	Weak transcription	Ovary	ovary
45	chr4:7874400-7875400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:7874400-7875600	Enhancers	HSMMtube	muscle
47	chr4:7874400-7877800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:7874400-7878000	Weak transcription	Fetal Kidney	kidney
49	chr4:7874400-7878000	Weak transcription	Left Ventricle	heart
50	chr4:7874400-7878200	Weak transcription	Brain Cingulate Gyrus	brain

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