Variant report

Variant	rs11544859
Chromosome Location	chr2:96933112-96933113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:180)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:180 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:96932904-96933168	GM12878	blood:	n/a	n/a
2	CTCF	chr2:96933000-96933150	AG09319	gingival:	n/a	n/a
3	MXI1	chr2:96930187-96933335	IMR90	lung:	n/a	n/a
4	CTCF	chr2:96933040-96933190	BE2_C	brain:	n/a	n/a
5	CTCF	chr2:96932980-96933130	K562	blood:	n/a	n/a
6	RAD21	chr2:96932764-96933357	HCT-116	colon:	n/a	n/a
7	ZNF384	chr2:96932737-96933173	GM12878	blood:	n/a	n/a
8	CTCF	chr2:96932953-96933143	GM10266	blood:	n/a	n/a
9	CTCF	chr2:96932872-96933240	GM12878	blood:	n/a	n/a
10	CTCF	chr2:96932982-96933127	GM13976	blood:	n/a	n/a
11	RAD21	chr2:96932802-96933304	MCF-7	breast:	n/a	n/a
12	CTCF	chr2:96932928-96933131	HUVEC	blood vessel:	n/a	n/a
13	SMC3	chr2:96932909-96933186	GM12878	blood:	n/a	n/a
14	CTCF	chr2:96932980-96933130	GM12874	blood:	n/a	n/a
15	RAD21	chr2:96932854-96933324	HepG2	liver:	n/a	n/a
16	ELF1	chr2:96932931-96933245	GM12878	blood:	n/a	n/a
17	CTCF	chr2:96932980-96933130	HBMEC	blood vessel:	n/a	n/a
18	CTCF	chr2:96932895-96933182	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr2:96933000-96933150	HUVEC	blood vessel:	n/a	n/a
20	MAZ	chr2:96932940-96933233	GM12878	blood:	n/a	n/a
21	CTCF	chr2:96932980-96933130	GM12871	blood:	n/a	n/a
22	CTCF	chr2:96932980-96933130	AoAF	blood vessel:	n/a	n/a
23	CTCF	chr2:96932836-96933245	K562	blood:	n/a	n/a
24	CTCF	chr2:96932975-96933146	GM19239	blood:	n/a	n/a
25	RAD21	chr2:96932849-96933190	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr2:96932980-96933130	HPF	lung:	n/a	n/a
27	SMC3	chr2:96932871-96933266	HepG2	liver:	n/a	n/a
28	GTF2F1	chr2:96933005-96933144	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr2:96933020-96933170	HPAF	blood vessel:	n/a	n/a
30	ZNF143	chr2:96932922-96933244	GM12878	blood:	n/a	n/a
31	CTCF	chr2:96932882-96933350	K562	blood:	n/a	n/a
32	RAD21	chr2:96932833-96933260	HepG2	liver:	n/a	n/a
33	YY1	chr2:96932916-96933195	GM12878	blood:	n/a	n/a
34	ZNF384	chr2:96932919-96933164	K562	blood:	n/a	n/a
35	CTCF	chr2:96933000-96933150	SK-N-SH_RA	brain:	n/a	n/a
36	CTCF	chr2:96932945-96933194	MCF-7	breast:	n/a	n/a
37	CTCF	chr2:96932956-96933171	GM12891	blood:	n/a	n/a
38	CTCF	chr2:96933020-96933170	HBMEC	blood vessel:	n/a	n/a
39	CTCF	chr2:96932980-96933130	HEK293	kidney:	n/a	n/a
40	CTCF	chr2:96932941-96933159	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:96932861-96933800	GM12878	blood:	n/a	n/a
42	CTCF	chr2:96932980-96933130	HMEC	breast:	n/a	n/a
43	CTCF	chr2:96932980-96933130	GM12869	blood:	n/a	n/a
44	ZMIZ1	chr2:96932933-96933193	K562	blood:	n/a	n/a
45	RCOR1	chr2:96932929-96933287	K562	blood:	n/a	n/a
46	CTCF	chr2:96932958-96933161	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr2:96932875-96933131	A549	lung:	n/a	n/a
48	CTCF	chr2:96933000-96933150	NHDF-neo	bronchial:	n/a	n/a
49	CTCF	chr2:96932969-96933148	GM10248	blood:	n/a	n/a
50	RAD21	chr2:96932894-96933185	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96807683..96808209-chr2:96932599..96933171,2	K562	blood:
2	chr2:96923812..96929557-chr2:96929618..96934014,11	K562	blood:
3	chr2:96929992..96934856-chr2:96999935..97004454,8	K562	blood:
4	chr2:96871739..96877156-chr2:96928674..96935050,17	K562	blood:
5	chr2:96781170..96783829-chr2:96932925..96934478,2	MCF-7	breast:
6	chr2:96930218..96933448-chr2:96968870..96972894,6	MCF-7	breast:
7	chr2:96930374..96934423-chr2:97000506..97002803,4	MCF-7	breast:
8	chr2:96868913..96876440-chr2:96928017..96934530,23	K562	blood:
9	chr2:96932066..96934505-chr2:97010263..97012552,2	MCF-7	breast:
10	chr2:96928652..96934635-chr2:96966746..96973769,11	K562	blood:
11	chr2:96930148..96938607-chr2:96966008..96973188,21	MCF-7	breast:
12	chr2:96871572..96876906-chr2:96928916..96935631,15	MCF-7	breast:
13	chr2:96870309..96876262-chr2:96928720..96933891,16	MCF-7	breast:
14	chr2:96929774..96935946-chr2:96940519..96946631,7	K562	blood:
15	chr2:96809057..96813419-chr2:96930542..96933437,6	MCF-7	breast:
16	chr2:96930650..96934516-chr2:96954888..96957639,4	MCF-7	breast:
17	chr2:96931524..96933198-chr2:96984671..96987602,2	K562	blood:

No data

Variant related genes	Relation type
TMEM127	TF binding region
ENSG00000135956	Chromatin interaction
ENSG00000230747	Chromatin interaction
ENSG00000158050	Chromatin interaction
ENSG00000228873	Chromatin interaction
ENSG00000121152	Chromatin interaction
ENSG00000144028	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000222040	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12623853	1.00[CHD][hapmap]
rs13416784	1.00[CHD][hapmap]
rs15005	1.00[CHD][hapmap]

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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96929800-96933200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr2:96930400-96933400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr2:96930600-96933200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:96930600-96933200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:96930600-96933200	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr2:96930800-96933200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:96930800-96933200	Active TSS	A549	lung
8	chr2:96930800-96933400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:96931000-96933200	Active TSS	Brain Germinal Matrix	brain
10	chr2:96931200-96933200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
11	chr2:96931600-96933600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
12	chr2:96932200-96933200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr2:96932200-96933200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr2:96932200-96933400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:96932200-96933800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:96932400-96933200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr2:96932400-96933200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:96932400-96933200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr2:96932400-96933200	Flanking Active TSS	Liver	Liver
20	chr2:96932400-96933200	Flanking Active TSS	Fetal Thymus	thymus
21	chr2:96932400-96933200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr2:96932600-96933200	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:96932600-96933200	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr2:96932600-96933200	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr2:96932600-96933200	Enhancers	Spleen	Spleen
26	chr2:96932600-96933400	Enhancers	Fetal Brain Male	brain
27	chr2:96932600-96933600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr2:96932600-96933600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:96932600-96933600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr2:96932600-96933600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:96932600-96933600	Enhancers	Stomach Mucosa	stomach
32	chr2:96932600-96934000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr2:96932600-96934200	Weak transcription	Aorta	Aorta
34	chr2:96932600-96941600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:96932800-96933200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:96932800-96933200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:96932800-96933200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:96932800-96933200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:96932800-96933200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
40	chr2:96932800-96933200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:96932800-96933200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:96932800-96933200	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr2:96932800-96933200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr2:96932800-96933200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr2:96932800-96933200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr2:96932800-96933200	Flanking Active TSS	HUVEC	blood vessel
47	chr2:96932800-96933200	Flanking Active TSS	Osteobl	bone
48	chr2:96932800-96933400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:96932800-96933400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr2:96932800-96933400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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