Variant report

Variant	rs6432060
Chromosome Location	chr2:10231938-10231939
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:10231820-10232050	GM12871	blood:	n/a	n/a
2	CTCF	chr2:10231892-10232038	GM10248	blood:	n/a	n/a
3	CTCF	chr2:10231900-10232050	GM12867	blood:	n/a	n/a
4	TBP	chr2:10231807-10232157	GM12878	blood:	n/a	n/a
5	CTCF	chr2:10231782-10232173	GM12878	blood:	n/a	n/a
6	MXI1	chr2:10231859-10232059	GM12878	blood:	n/a	n/a
7	CTCF	chr2:10231900-10232050	RPTEC	kidney:	n/a	n/a
8	POLR2A	chr2:10231795-10231984	GM12878	blood:	n/a	n/a
9	CTCF	chr2:10231840-10231990	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:10231277-10232056	GM19193	blood:	n/a	n/a
11	SP1	chr2:10231833-10232298	GM12878	blood:	n/a	n/a
12	CTCF	chr2:10231900-10232050	GM12864	blood:	n/a	n/a
13	CTCF	chr2:10231820-10231970	GM12869	blood:	n/a	n/a
14	POLR2A	chr2:10231221-10232112	GM19099	blood:	n/a	n/a
15	CTCF	chr2:10231920-10232070	GM12869	blood:	n/a	n/a
16	CTCF	chr2:10231880-10232030	HRE	kidney:	n/a	n/a
17	CTCF	chr2:10231878-10231949	Spleen_OC	spleen:	n/a	n/a
18	CTCF	chr2:10231900-10232050	GM12872	blood:	n/a	n/a
19	MAZ	chr2:10231806-10231942	GM12878	blood:	n/a	n/a
20	SMC3	chr2:10231769-10232116	GM12878	blood:	n/a	n/a
21	ZNF143	chr2:10231470-10232115	GM12878	blood:	n/a	n/a
22	EBF1	chr2:10231728-10232058	GM12878	blood:	n/a	n/a
23	CTCF	chr2:10231901-10232067	GM12878	blood:	n/a	n/a
24	CTCF	chr2:10231880-10232030	GM12873	blood:	n/a	n/a
25	MAX	chr2:10231372-10232035	GM12878	blood:	n/a	n/a
26	CTCF	chr2:10231860-10232010	HRE	kidney:	n/a	n/a
27	NFYB	chr2:10231892-10232833	GM12878	blood:	n/a	chr2:10232097-10232112 chr2:10232138-10232153
28	CTCF	chr2:10231880-10232030	RPTEC	kidney:	n/a	n/a
29	CTCF	chr2:10231888-10232042	Kidney_OC	kidney:	n/a	n/a
30	CTCF	chr2:10231787-10232052	GM19239	blood:	n/a	n/a
31	BHLHE40	chr2:10231926-10232013	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:10231242-10232028	GM18526	blood:	n/a	n/a
33	POLR2A	chr2:10231261-10232050	GM18951	blood:	n/a	n/a
34	CTCF	chr2:10231880-10232030	GM12872	blood:	n/a	n/a
35	CTCF	chr2:10231885-10232035	GM12892	blood:	n/a	n/a
36	CTCF	chr2:10231880-10232030	GM12878	blood:	n/a	n/a
37	CTCF	chr2:10231912-10232027	Pancreas_OC	pancreas:	n/a	n/a
38	CTCF	chr2:10231880-10232030	GM12864	blood:	n/a	n/a
39	PAX5	chr2:10231866-10232034	GM12878	blood:	n/a	n/a
40	CTCF	chr2:10231889-10232056	GM10266	blood:	n/a	n/a
41	RAD21	chr2:10231791-10232111	GM12878	blood:	n/a	n/a
42	PAX5	chr2:10231205-10232077	GM12878	blood:	n/a	n/a
43	CTCF	chr2:10231890-10232041	GM12891	blood:	n/a	n/a
44	PAX5	chr2:10231825-10231997	GM12892	blood:	n/a	n/a
45	CTCF	chr2:10231820-10231970	GM12871	blood:	n/a	n/a
46	CHD2	chr2:10231840-10232156	GM12878	blood:	n/a	n/a
47	TCF3	chr2:10231618-10232080	GM12878	blood:	n/a	n/a
48	CTCF	chr2:10231920-10232070	GM12870	blood:	n/a	n/a
49	CTCF	chr2:10231875-10232027	GM19238	blood:	n/a	n/a
50	SP1	chr2:10231913-10232309	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10231244..10232877-chr2:10442178..10444035,2	K562	blood:
2	chr2:10229570..10233123-chr2:10259464..10263291,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000212558	TF binding region
ENSG00000272524	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000115756	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10177872	1.00[ASN][1000 genomes]
rs10929632	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886661	1.00[ASN][1000 genomes]
rs12992149	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13400128	1.00[ASN][1000 genomes]
rs3935840	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302193	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321336	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485541	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569449	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669527	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669528	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6432058	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786623	1.00[ASN][1000 genomes]
rs72786624	1.00[ASN][1000 genomes]
rs7587317	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587529	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602408	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1007965	chr2:10154960-10276125	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1014790	chr2:10156968-10274855	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv999019	chr2:10157762-10273232	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
7	nsv873633	chr2:10175442-10266563	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv1010706	chr2:10189219-10266995	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6432060	CYS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10230800-10232000	Flanking Active TSS	GM12878-XiMat	blood
2	chr2:10231000-10232000	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr2:10231200-10232000	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr2:10231200-10232000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
5	chr2:10231200-10232000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:10231200-10232000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:10231200-10232000	Enhancers	Pancreas	Pancrea
8	chr2:10231200-10232200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr2:10231400-10232000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
11	chr2:10231400-10232000	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr2:10231400-10232000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr2:10231400-10232000	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
15	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:10231400-10232000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:10231400-10232000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
22	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
23	chr2:10231400-10232000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
24	chr2:10231400-10232000	ZNF genes & repeats	Lung	lung
25	chr2:10231400-10232000	Bivalent/Poised TSS	Psoas Muscle	Psoas
26	chr2:10231400-10232000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
27	chr2:10231400-10232000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
28	chr2:10231400-10232000	Bivalent/Poised TSS	Thymus	Thymus
29	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr2:10231400-10236600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:10231600-10232000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr2:10231600-10232000	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr2:10231600-10232000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
34	chr2:10231600-10232000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:10231600-10232000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:10231600-10232000	Bivalent/Poised TSS	Liver	Liver
37	chr2:10231600-10232000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
38	chr2:10231600-10232000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
39	chr2:10231600-10232000	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
40	chr2:10231600-10232000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
41	chr2:10231600-10232000	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion
42	chr2:10231600-10232800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:10231800-10232000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:10231800-10232000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:10231800-10232000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:10231800-10232000	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
47	chr2:10231800-10232000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr2:10231800-10232000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:10231800-10232000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
50	chr2:10231800-10232000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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