Variant report

Variant	rs28901612
Chromosome Location	chr2:234838307-234838308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:234838262-234838357	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr2:234838260-234838410	HMF	breast:	n/a	n/a
3	CTCF	chr2:234838260-234838410	BE2_C	brain:	n/a	n/a
4	CTCF	chr2:234838280-234838430	AG04449	skin:	n/a	n/a
5	CTCF	chr2:234838300-234838450	HMEC	breast:	n/a	n/a
6	CTCF	chr2:234838302-234838454	MCF-7	breast:	n/a	n/a
7	CTCF	chr2:234838300-234838450	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr2:234838240-234838390	HCFaa	heart:	n/a	n/a
9	CTCF	chr2:234838300-234838450	AoAF	blood vessel:	n/a	n/a
10	CTCF	chr2:234838240-234838390	GM12875	blood:	n/a	n/a
11	CTCF	chr2:234838240-234838390	RPTEC	kidney:	n/a	n/a
12	CTCF	chr2:234838276-234838463	MCF-7	breast:	n/a	n/a
13	CTCF	chr2:234838240-234838390	HepG2	liver:	n/a	n/a
14	CTCF	chr2:234838220-234838370	RPTEC	kidney:	n/a	n/a
15	CTCF	chr2:234838260-234838410	HBMEC	blood vessel:	n/a	n/a
16	CTCF	chr2:234838260-234838410	HRE	kidney:	n/a	n/a
17	CTCF	chr2:234838240-234838390	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr2:234838300-234838450	HPAF	blood vessel:	n/a	n/a
19	MYC	chr2:234838181-234838324	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr2:234838260-234838410	NHEK	skin:	n/a	n/a
21	CTCF	chr2:234838280-234838430	HCPEpiC	choroid plexus:	n/a	n/a
22	CTCF	chr2:234838280-234838430	AoAF	blood vessel:	n/a	n/a
23	CTCF	chr2:234838280-234838430	A549	lung:	n/a	n/a
24	CTCF	chr2:234838260-234838410	HPAF	blood vessel:	n/a	n/a
25	CTCF	chr2:234838220-234838370	HCM	heart:	n/a	n/a
26	CTCF	chr2:234838300-234838450	BJ	skin:	n/a	n/a
27	CTCF	chr2:234838280-234838430	GM12864	blood:	n/a	n/a
28	CTCF	chr2:234838300-234838450	SAEC	small airway:	n/a	n/a
29	CTCF	chr2:234838260-234838410	HRPEpiC	eye:	n/a	n/a
30	CTCF	chr2:234838240-234838390	MCF-7	breast:	n/a	n/a
31	ZNF143	chr2:234838158-234838521	H1-hESC	embryonic stem cell:	n/a	chr2:234838322-234838337
32	CTCF	chr2:234838220-234838370	HRPEpiC	eye:	n/a	n/a
33	CTCF	chr2:234838280-234838430	HAc	cerebellar:	n/a	n/a
34	CTCF	chr2:234838260-234838410	GM12864	blood:	n/a	n/a
35	CTCF	chr2:234838079-234838453	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr2:234838280-234838430	AG09309	skin:	n/a	n/a
37	CTCF	chr2:234838300-234838450	GM12872	blood:	n/a	n/a
38	FOS	chr2:234838305-234838436	MCF10A-Er-Src	breast:	n/a	n/a
39	CTCF	chr2:234838280-234838430	HPF	lung:	n/a	n/a
40	CTCF	chr2:234838220-234838370	BE2_C	brain:	n/a	n/a
41	CTCF	chr2:234838285-234838391	MCF-7	breast:	n/a	n/a
42	CTCF	chr2:234838280-234838430	AG04450	lung:	n/a	n/a
43	CTCF	chr2:234838260-234838410	HA-sp	spinal cord:	n/a	n/a
44	JUND	chr2:234838219-234838478	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr2:234838300-234838450	AG09319	gingival:	n/a	n/a
46	CTCF	chr2:234838280-234838430	MCF-7	breast:	n/a	n/a
47	CTCF	chr2:234838260-234838410	GM12873	blood:	n/a	n/a
48	CTCF	chr2:234838260-234838410	HEK293	kidney:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234837551..234838340-chr2:235010553..235011295,2	MCF-7	breast:

No data

Variant related genes	Relation type
TRPM8	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11568316	1.00[AMR][1000 genomes]
rs28900714	1.00[JPT][hapmap]
rs28900723	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28900724	1.00[JPT][hapmap]
rs28900976	1.00[JPT][hapmap]
rs28901606	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs28901616	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28901617	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs28901622	1.00[YRI][hapmap]
rs28901623	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28901638	1.00[YRI][hapmap]
rs28902188	1.00[YRI][hapmap]
rs28902190	1.00[YRI][hapmap]
rs3771333	1.00[JPT][hapmap]
rs45619032	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234837000-234838400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:234837000-234838600	Enhancers	A549	lung
3	chr2:234837400-234839000	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr2:234837600-234838600	Enhancers	H9 Cell Line	embryonic stem cell
5	chr2:234837600-234838800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr2:234837600-234838800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr2:234837600-234839000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr2:234837600-234839000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr2:234837800-234838400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr2:234837800-234838800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr2:234837800-234839000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr2:234838000-234838400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:234838000-234838400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:234838000-234838400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:234838000-234838800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:234838000-234838800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:234838000-234838800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:234838000-234838800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:234838200-234838400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:234838200-234838400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:234838200-234838400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:234838200-234838400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:234838200-234838600	Active TSS	HSMMtube	muscle

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