Variant report

Variant	rs35827450
Chromosome Location	chr12:57606421-57606422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:57606320-57606470	AoAF	blood vessel:	n/a	n/a
2	CTCF	chr12:57606300-57606450	NB4	blood:	n/a	n/a
3	CTCF	chr12:57606280-57606430	K562	blood:	n/a	n/a
4	CTCF	chr12:57606380-57606530	AG09319	gingival:	n/a	n/a
5	CTCF	chr12:57606340-57606490	HVMF	connective:	n/a	n/a
6	CTCF	chr12:57606380-57606530	AoAF	blood vessel:	n/a	n/a
7	CTCF	chr12:57606311-57606478	K562	blood:	n/a	n/a
8	CTCF	chr12:57606360-57606510	HPAF	blood vessel:	n/a	n/a
9	POLR2A	chr12:57604356-57606823	U87	brain:	n/a	n/a
10	CTCFL	chr12:57606315-57606467	K562	blood:	n/a	n/a
11	CTCF	chr12:57606339-57606506	K562	blood:	n/a	n/a
12	CTCF	chr12:57606280-57606430	HCM	heart:	n/a	n/a
13	CTCF	chr12:57606300-57606450	HVMF	connective:	n/a	n/a
14	CTCF	chr12:57606240-57606556	K562	blood:	n/a	n/a
15	CTCF	chr12:57606400-57606550	HCFaa	heart:	n/a	n/a
16	CTCF	chr12:57606320-57606470	K562	blood:	n/a	n/a
17	CTCF	chr12:57606226-57606582	K562	blood:	n/a	n/a
18	CTCF	chr12:57606279-57609127	SK-N-SH	brain:	n/a	chr12:57608634-57608647 chr12:57608636-57608646 chr12:57608254-57608263 chr12:57608631-57608649 chr12:57608633-57608654 chr12:57607238-57607247 chr12:57607235-57607253 chr12:57608251-57608269 chr12:57607237-57607258 chr12:57608252-57608268 chr12:57608634-57608643
19	CTCF	chr12:57606280-57606430	NHDF-neo	bronchial:	n/a	n/a
20	CTCF	chr12:57606144-57606680	K562	blood:	n/a	n/a
21	CTCF	chr12:57606380-57606530	BJ	skin:	n/a	n/a
22	CTCF	chr12:57606400-57606550	BJ	skin:	n/a	n/a
23	CTCF	chr12:57606280-57606430	HCPEpiC	choroid plexus:	n/a	n/a
24	CTCF	chr12:57606380-57606530	HBMEC	blood vessel:	n/a	n/a
25	CTCF	chr12:57606320-57606470	AG10803	skin:	n/a	n/a
26	CTCF	chr12:57606280-57606430	AG09309	skin:	n/a	n/a
27	POLR2A	chr12:57604308-57606829	U87	brain:	n/a	n/a
28	CTCF	chr12:57606360-57606510	AG04449	skin:	n/a	n/a
29	CTCF	chr12:57606363-57606426	Fibrobl	skin:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57586695..57588801-chr12:57605847..57608117,2	MCF-7	breast:
2	chr12:57480154..57482467-chr12:57605881..57608725,2	K562	blood:
3	chr12:57606014..57610025-chr12:57631623..57633806,36	MCF-7	breast:
4	chr12:57603444..57607187-chr12:57608287..57611860,5	K562	blood:
5	chr12:57599755..57603082-chr12:57604148..57606889,3	K562	blood:
6	chr12:57531973..57533574-chr12:57605011..57607679,2	MCF-7	breast:
7	chr12:57598445..57603565-chr12:57603905..57607963,7	K562	blood:
8	chr12:57578786..57581016-chr12:57606054..57608817,2	MCF-7	breast:
9	chr12:57602021..57603919-chr12:57605356..57607046,2	MCF-7	breast:
10	chr12:57606205..57609184-chr12:57636393..57638193,29	MCF-7	breast:

No data

Variant related genes	Relation type
NXPH4	TF binding region
ENSG00000166881	Chromatin interaction
ENSG00000182379	Chromatin interaction
ENSG00000221365	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10083191	0.83[AFR][1000 genomes]
rs11172151	0.83[AFR][1000 genomes]
rs11557168	1.00[MEX][hapmap]
rs12297756	1.00[CEU][hapmap]
rs12299952	0.83[AFR][1000 genomes]
rs12310527	0.83[LWK][hapmap]
rs12310686	0.95[AFR][1000 genomes]
rs12312567	0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[AFR][1000 genomes]
rs12312780	0.88[LWK][hapmap];0.96[AFR][1000 genomes]
rs12317897	0.83[AFR][1000 genomes]
rs12320772	0.83[AFR][1000 genomes]
rs34100010	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers 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 miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv525873	chr12:57535266-57616013	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv869636	chr12:57590172-57613714	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv899116	chr12:57597169-57623363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57541600-57606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:57541800-57607400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:57552800-57606800	Strong transcription	Fetal Intestine Large	intestine
4	chr12:57552800-57607000	Strong transcription	Liver	Liver
5	chr12:57553200-57607400	Strong transcription	Fetal Intestine Small	intestine
6	chr12:57557400-57606800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr12:57560800-57606600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:57565800-57606600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:57570200-57606800	Strong transcription	Fetal Stomach	stomach
10	chr12:57570600-57606800	Strong transcription	Osteobl	bone
11	chr12:57576800-57606600	Strong transcription	HepG2	liver
12	chr12:57576800-57607000	Strong transcription	Brain Germinal Matrix	brain
13	chr12:57577000-57606600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:57577000-57606800	Strong transcription	Colonic Mucosa	Colon
15	chr12:57577000-57606800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:57577000-57606800	Strong transcription	Ovary	ovary
17	chr12:57577200-57606600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:57577200-57606800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:57577200-57606800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:57577200-57606800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:57577200-57606800	Weak transcription	A549	lung
22	chr12:57577400-57606600	Strong transcription	Esophagus	oesophagus
23	chr12:57577600-57606800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:57577600-57607200	Weak transcription	NHEK	skin
25	chr12:57582600-57607200	Weak transcription	HMEC	breast
26	chr12:57584400-57606800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:57585800-57606800	Strong transcription	Gastric	stomach
28	chr12:57585800-57607200	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr12:57585800-57608600	Strong transcription	NHLF	lung
30	chr12:57587200-57606800	Strong transcription	Adipose Nuclei	Adipose
31	chr12:57587400-57606600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:57592000-57606800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:57592400-57606600	Strong transcription	Spleen	Spleen
34	chr12:57598600-57607400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:57600400-57606800	Weak transcription	Pancreas	Pancrea
36	chr12:57600600-57606600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:57600600-57606600	Strong transcription	Placenta	Placenta
38	chr12:57600600-57607400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:57601400-57606800	Weak transcription	Stomach Mucosa	stomach
40	chr12:57601800-57606800	Strong transcription	Fetal Brain Female	brain
41	chr12:57601800-57608000	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr12:57603000-57606600	Weak transcription	Fetal Brain Male	brain
43	chr12:57603200-57606800	Strong transcription	Fetal Muscle Leg	muscle
44	chr12:57603200-57610200	Weak transcription	Right Atrium	heart
45	chr12:57603400-57606600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:57603400-57606600	Strong transcription	Right Ventricle	heart
47	chr12:57603400-57607200	Weak transcription	Fetal Heart	heart
48	chr12:57603600-57606800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:57603600-57607400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:57603800-57607400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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