Variant report

Variant	rs6890853
Chromosome Location	chr5:35852311-35852312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:106)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:106 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:35852260-35852410	NHEK	skin:	n/a	n/a
2	CTCF	chr5:35852260-35852410	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr5:35852200-35852350	AG10803	skin:	n/a	n/a
4	RAD21	chr5:35852070-35852589	MCF-7	breast:	n/a	chr5:35852438-35852447 chr5:35852109-35852123
5	CTCF	chr5:35852280-35852430	HBMEC	blood vessel:	n/a	n/a
6	CTCF	chr5:35852280-35852430	GM12874	blood:	n/a	n/a
7	CTCF	chr5:35852240-35852390	HA-sp	spinal cord:	n/a	n/a
8	RAD21	chr5:35852234-35852433	HepG2	liver:	n/a	n/a
9	CTCF	chr5:35852202-35852472	MCF-7	breast:	n/a	n/a
10	CTCF	chr5:35852180-35852330	HA-sp	spinal cord:	n/a	n/a
11	CTCF	chr5:35852220-35852370	GM12866	blood:	n/a	n/a
12	CTCF	chr5:35852271-35852422	GM12892	blood:	n/a	n/a
13	CTCF	chr5:35852280-35852430	GM12864	blood:	n/a	n/a
14	CTCF	chr5:35852180-35852330	HPF	lung:	n/a	n/a
15	CTCF	chr5:35852254-35852417	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr5:35852209-35852446	IMR90	lung:	n/a	n/a
17	CTCF	chr5:35852280-35852430	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr5:35852260-35852410	GM12865	blood:	n/a	n/a
19	POLR2A	chr5:35852154-35852514	Gliobla	brain:	n/a	n/a
20	FOS	chr5:35852254-35852834	MCF10A-Er-Src	breast:	n/a	chr5:35852382-35852394 chr5:35852384-35852392 chr5:35852775-35852785
21	CTCF	chr5:35852260-35852410	WERI-Rb-1	eye:	n/a	n/a
22	RAD21	chr5:35852222-35852490	SK-N-SH_RA	brain:	n/a	chr5:35852438-35852447
23	ZNF143	chr5:35852262-35852395	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr5:35852280-35852430	HCT-116	colon:	n/a	n/a
25	CTCF	chr5:35852200-35852350	A549	lung:	n/a	n/a
26	CTCF	chr5:35852179-35852483	MCF-7	breast:	n/a	n/a
27	CTCF	chr5:35852280-35852430	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr5:35852260-35852410	RPTEC	kidney:	n/a	n/a
29	CTCF	chr5:35852260-35852410	GM12875	blood:	n/a	n/a
30	RAD21	chr5:35852256-35852467	Hela-S3	cervix:	n/a	chr5:35852438-35852447
31	CTCF	chr5:35852184-35852484	MCF-7	breast:	n/a	n/a
32	EBF1	chr5:35852231-35852930	GM12878	blood:	n/a	n/a
33	CTCF	chr5:35852269-35852396	ProgFib	skin:	n/a	n/a
34	CTCF	chr5:35852195-35852456	A549	lung:	n/a	n/a
35	CTCF	chr5:35852300-35852450	AG04449	skin:	n/a	n/a
36	CTCF	chr5:35852220-35852370	Caco-2	colon:	n/a	n/a
37	CTCF	chr5:35852280-35852430	BJ	skin:	n/a	n/a
38	FOS	chr5:35852301-35852662	MCF10A-Er-Src	breast:	n/a	chr5:35852382-35852394 chr5:35852384-35852392
39	CTCF	chr5:35851967-35852711	SK-N-SH	brain:	n/a	chr5:35852108-35852116
40	CTCF	chr5:35852280-35852430	HepG2	liver:	n/a	n/a
41	CTCF	chr5:35852231-35852434	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr5:35852180-35852330	HRE	kidney:	n/a	n/a
43	CTCF	chr5:35852280-35852430	MCF-7	breast:	n/a	n/a
44	CTCF	chr5:35852241-35852447	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr5:35852200-35852350	GM12865	blood:	n/a	n/a
46	MYC	chr5:35852260-35852415	MCF-7	breast:	n/a	n/a
47	CTCF	chr5:35852260-35852410	HFF	foreskin:	n/a	n/a
48	CTCF	chr5:35852220-35852370	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr5:35852300-35852450	HRE	kidney:	n/a	n/a
50	POLR2A	chr5:35852300-35852468	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:35852286-35852336	K562	blood:	n/a
2	chr5:35852286-35852336	NB4	blood:	n/a
3	chr5:35852286-35852336	HRE	kidney:	n/a
4	chr5:35852286-35852336	AoSMC	blood vessel:	n/a
5	chr5:35852286-35852336	SK-N-SH	brain:	n/a
6	chr5:35852286-35852336	SK-N-SH_RA	brain:	n/a
7	chr5:35852286-35852336	T-47D	breast:	n/a
8	chr5:35852286-35852336	SAEC	small airway:	n/a
9	chr5:35852286-35852336	AG09319	gingival:	n/a
10	chr5:35852286-35852336	AG04450	lung:	fetal
11	chr5:35852286-35852336	HIPEpiC	eye:	n/a
12	chr5:35852286-35852336	Caco-2	colon:	n/a
13	chr5:35852286-35852336	PANC-1	pancreas:	n/a
14	chr5:35852286-35852336	Hela-S3	cervix:	n/a
15	chr5:35852286-35852336	HMEC	breast:	n/a
16	chr5:35852286-35852336	SKMC	muscle:	n/a
17	chr5:35852286-35852336	GM19239	blood:	n/a
18	chr5:35852286-35852336	Jurkat	blood:	n/a
19	chr5:35852286-35852336	AG04449	skin:	fetal
20	chr5:35852286-35852336	HNPCEpiC	eye:	n/a
21	chr5:35852286-35852336	HCPEpiC	choroid plexus:	n/a
22	chr5:35852286-35852336	SK-N-MC	brain:	n/a
23	chr5:35852286-35852336	Hepatocyte	liver:	n/a
24	chr5:35852286-35852336	AG10803	skin:	n/a
25	chr5:35852286-35852336	HepG2	liver:	n/a
26	chr5:35852286-35852336	BJ	skin:	n/a
27	chr5:35852286-35852336	NH-A	brain:	n/a
28	chr5:35852286-35852336	ovcar-3	ovarian:	n/a
29	chr5:35852286-35852336	LNCaP	prostate:	n/a
30	chr5:35852286-35852336	GM06990	blood:	n/a
31	chr5:35852286-35852336	HRPEpiC	eye:	n/a
32	chr5:35852286-35852336	NHBE	bronchial:	n/a
33	chr5:35852286-35852336	GM12891	blood:	n/a
34	chr5:35852286-35852336	HCT-116	colon:	n/a
35	chr5:35852286-35852336	HCM	heart:	n/a
36	chr5:35852286-35852336	AG09309	skin:	n/a
37	chr5:35852286-35852336	RPTEC	kidney:	n/a
38	chr5:35852286-35852336	HPAEpiC	pulmonary alveolar:	n/a
39	chr5:35852286-35852336	HUVEC	blood vessel:	n/a
40	chr5:35852286-35852336	HL-60	blood:	n/a
41	chr5:35852286-35852336	H1-hESC	embryonic stem cell:	embryo
42	chr5:35852286-35852336	PrEC	prostate:	n/a
43	chr5:35852286-35852336	BE2_C	brain:	n/a
44	chr5:35852286-35852336	HEEpiC	esophagus:	n/a
45	chr5:35852286-35852336	ECC-1	luminal epithelium:	n/a
46	chr5:35852286-35852336	HRCEpiC	kidney:	n/a
47	chr5:35852286-35852336	MCF-7	breast:	n/a
48	chr5:35852286-35852336	A549	lung:	n/a
49	chr5:35852286-35852336	IMR90	lung:	fetal
50	chr5:35852286-35852336	HAEpiC	amniotic membrane:	n/a

No data

Variant related genes	Relation type
IL7R	TF binding region
IL7R	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10063294	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs10213865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10214237	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10214273	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10472984	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11567694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11567705	0.83[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742240	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11742270	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13188960	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34463936	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4594881	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62351975	0.80[EUR][1000 genomes]
rs6871748	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6881270	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6881706	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6897932	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7717955	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs987106	0.88[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv881055	chr5:35850693-35858721	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv881685	chr5:35850693-35859863	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv881358	chr5:35850693-35861068	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv880610	chr5:35850693-35866265	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv880517	chr5:35850693-35870814	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Primary biliary cirrhosis	23000144	GWAS catalog

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35848800-35852400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr5:35849600-35856200	Enhancers	Dnd41	blood
3	chr5:35849800-35852600	Enhancers	Primary T cells fromperipheralblood	blood
4	chr5:35849800-35852800	Enhancers	Thymus	Thymus
5	chr5:35849800-35853200	Enhancers	Fetal Thymus	thymus
6	chr5:35850000-35852600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr5:35851000-35853000	Flanking Active TSS	Osteobl	bone
8	chr5:35851200-35853000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:35851400-35852800	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr5:35851600-35852400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:35851600-35852400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:35851600-35852400	Enhancers	Adipose Nuclei	Adipose
13	chr5:35851600-35852400	Enhancers	Placenta	Placenta
14	chr5:35851600-35852400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr5:35851600-35852600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:35851600-35852600	Enhancers	HSMMtube	muscle
17	chr5:35851600-35852600	Enhancers	NHEK	skin
18	chr5:35851600-35852800	Enhancers	HMEC	breast
19	chr5:35851600-35853000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:35851800-35852400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:35851800-35852600	Enhancers	Psoas Muscle	Psoas
22	chr5:35851800-35852800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:35851800-35852800	Enhancers	Duodenum Mucosa	Duodenum
24	chr5:35851800-35852800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr5:35851800-35853000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:35851800-35853000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:35851800-35853000	Enhancers	Ovary	ovary
28	chr5:35851800-35853000	Enhancers	NHLF	lung
29	chr5:35851800-35853200	Enhancers	GM12878-XiMat	blood
30	chr5:35851800-35856800	Enhancers	NHDF-Ad	bronchial
31	chr5:35852000-35852400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr5:35852000-35852400	Flanking Active TSS	Hela-S3	cervix
33	chr5:35852000-35852600	Enhancers	Left Ventricle	heart
34	chr5:35852000-35852800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:35852000-35853000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr5:35852000-35853000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:35852000-35853000	ZNF genes & repeats	Right Atrium	heart
38	chr5:35852000-35853200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:35852000-35853400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr5:35852000-35853400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:35852000-35853600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:35852000-35853800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:35852000-35854400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:35852000-35854600	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr5:35852000-35856800	Enhancers	Primary B cells from cord blood	blood
46	chr5:35852200-35852400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr5:35852200-35852400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr5:35852200-35852400	Enhancers	A549	lung
49	chr5:35852200-35852800	Flanking Active TSS	HSMM	muscle
50	chr5:35852200-35853400	Enhancers	Primary B cells from peripheral blood	blood

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