Variant report

Variant	rs11695996
Chromosome Location	chr2:100854336-100854337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr2:100854213-100854475	GM12878	blood:	n/a	chr2:100854339-100854350
2	CTCF	chr2:100854301-100854497	MCF-7	breast:	n/a	n/a
3	CTCF	chr2:100854320-100854470	WERI-Rb-1	eye:	n/a	n/a
4	CTCF	chr2:100854200-100854350	BE2_C	brain:	n/a	n/a
5	CTCF	chr2:100854280-100854430	GM12873	blood:	n/a	n/a
6	CTCF	chr2:100854300-100854450	NB4	blood:	n/a	n/a
7	CTCF	chr2:100854331-100854458	K562	blood:	n/a	n/a
8	CTCF	chr2:100854264-100854538	K562	blood:	n/a	n/a
9	CTCF	chr2:100854295-100854487	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr2:100854238-100854493	K562	blood:	n/a	n/a
11	CTCF	chr2:100854303-100854470	GM12878	blood:	n/a	n/a
12	CTCF	chr2:100854280-100854430	HRE	kidney:	n/a	n/a
13	CTCF	chr2:100854320-100854463	MCF-7	breast:	n/a	n/a
14	MAX	chr2:100854249-100854585	NB4	blood:	n/a	n/a
15	CTCF	chr2:100854300-100854450	HepG2	liver:	n/a	n/a
16	CTCF	chr2:100854300-100854450	HEK293	kidney:	n/a	n/a
17	CTCF	chr2:100854280-100854430	GM06990	blood:	n/a	n/a
18	CTCF	chr2:100854260-100854410	HCT-116	colon:	n/a	n/a
19	CTCF	chr2:100854333-100854441	MCF-7	breast:	n/a	n/a
20	CTCF	chr2:100854300-100854450	GM12874	blood:	n/a	n/a
21	CTCF	chr2:100854320-100854470	GM12873	blood:	n/a	n/a
22	CTCF	chr2:100854240-100854390	GM12864	blood:	n/a	n/a
23	CTCF	chr2:100854300-100854450	GM12868	blood:	n/a	n/a
24	CTCF	chr2:100854331-100854448	GM19238	blood:	n/a	n/a
25	CTCF	chr2:100854280-100854430	A549	lung:	n/a	n/a
26	CTCF	chr2:100854320-100854470	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr2:100854280-100854430	GM12866	blood:	n/a	n/a
28	ZNF143	chr2:100854256-100854389	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr2:100854220-100854370	GM12864	blood:	n/a	n/a
30	CTCF	chr2:100854320-100854470	GM12878	blood:	n/a	n/a
31	RAD21	chr2:100854181-100854608	H1-hESC	embryonic stem cell:	n/a	chr2:100854581-100854594
32	CTCF	chr2:100854300-100854450	GM12873	blood:	n/a	n/a
33	CTCF	chr2:100854300-100854450	GM12875	blood:	n/a	n/a
34	ZNF263	chr2:100854259-100854616	HEK293-T-REx	kidney:	n/a	chr2:100854414-100854435 chr2:100854428-100854437
35	CTCF	chr2:100854280-100854430	GM12865	blood:	n/a	n/a
36	CTCF	chr2:100854240-100854390	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr2:100854268-100854644	K562	blood:	n/a	n/a
38	CTCF	chr2:100854320-100854470	GM12866	blood:	n/a	n/a
39	CTCF	chr2:100854280-100854430	GM12869	blood:	n/a	n/a
40	RAD21	chr2:100854321-100854494	IMR90	lung:	n/a	n/a
41	CTCF	chr2:100854300-100854450	SK-N-SH_RA	brain:	n/a	n/a
42	CTCF	chr2:100854300-100854450	HCT-116	colon:	n/a	n/a
43	CTCF	chr2:100854260-100854410	HA-sp	spinal cord:	n/a	n/a
44	CTCF	chr2:100854320-100854470	GM12872	blood:	n/a	n/a
45	CTCF	chr2:100854240-100854390	HFF-Myc	foreskin:	n/a	n/a
46	CTCF	chr2:100854260-100854410	GM12878	blood:	n/a	n/a

No data

Variant related genes	Relation type
LINC01104	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10496345	0.81[EUR][1000 genomes]
rs10496346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10865037	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123817	0.84[EUR][1000 genomes]
rs11123818	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123819	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123820	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123821	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123823	1.00[YRI][hapmap]
rs1122231	0.84[EUR][1000 genomes]
rs1160543	0.83[EUR][1000 genomes]
rs1160545	0.83[EUR][1000 genomes]
rs11684761	0.82[EUR][1000 genomes]
rs11685491	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11686372	0.82[EUR][1000 genomes]
rs11687241	0.87[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11689199	0.86[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs11689201	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11690335	0.82[EUR][1000 genomes]
rs11691409	0.82[EUR][1000 genomes]
rs11693324	0.82[EUR][1000 genomes]
rs11694723	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11695383	0.82[EUR][1000 genomes]
rs12053126	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12614880	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12615145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619178	0.84[EUR][1000 genomes]
rs12987662	0.82[EUR][1000 genomes]
rs12990462	0.82[EUR][1000 genomes]
rs12991254	0.81[EUR][1000 genomes]
rs12992090	0.81[EUR][1000 genomes]
rs12994592	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13010010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13013169	0.80[EUR][1000 genomes]
rs13017207	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13018640	0.82[EUR][1000 genomes]
rs13019179	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs13026143	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13026283	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13034176	0.83[EUR][1000 genomes]
rs1465800	0.84[EUR][1000 genomes]
rs1465801	0.84[EUR][1000 genomes]
rs2309812	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2309838	0.84[EUR][1000 genomes]
rs2871344	0.84[EUR][1000 genomes]
rs4303732	0.83[EUR][1000 genomes]
rs4331524	0.81[AFR][1000 genomes]
rs4583487	0.83[EUR][1000 genomes]
rs4622752	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4851264	0.80[EUR][1000 genomes]
rs4851266	0.81[EUR][1000 genomes]
rs4851267	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4851268	0.82[EUR][1000 genomes]
rs4851270	0.83[EUR][1000 genomes]
rs4851271	0.83[EUR][1000 genomes]
rs6709656	0.80[EUR][1000 genomes]
rs6750097	0.84[EUR][1000 genomes]
rs6750505	0.80[EUR][1000 genomes]
rs7566527	0.80[EUR][1000 genomes]
rs893246	0.81[EUR][1000 genomes]
rs999052	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100849400-100856000	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:100851000-100854600	Enhancers	Fetal Thymus	thymus
3	chr2:100851000-100855400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:100851200-100854800	Enhancers	Primary T cells fromperipheralblood	blood
5	chr2:100851200-100855200	Enhancers	Thymus	Thymus
6	chr2:100851600-100854600	Enhancers	Primary T cells from cord blood	blood
7	chr2:100851600-100855200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:100851800-100854800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:100851800-100855800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:100851800-100859200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:100852000-100857000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:100852000-100859000	Weak transcription	Lung	lung
13	chr2:100852200-100855800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:100852400-100859000	Weak transcription	Spleen	Spleen
15	chr2:100852600-100855400	Enhancers	Primary B cells from cord blood	blood
16	chr2:100852800-100854600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:100853400-100854600	Enhancers	Fetal Heart	heart
18	chr2:100853400-100856600	Enhancers	Fetal Brain Male	brain
19	chr2:100853600-100854600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:100853600-100855400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:100853600-100856200	Enhancers	Brain Germinal Matrix	brain
22	chr2:100853800-100855200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:100853800-100859200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:100854000-100855000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:100854000-100855200	Weak transcription	Fetal Kidney	kidney
26	chr2:100854000-100858600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:100854200-100855200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr2:100854200-100856000	Weak transcription	Fetal Lung	lung

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