Variant report

Variant	rs7420169
Chromosome Location	chr2:182548671-182548672
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr2:182547872-182549023	H1-hESC	embryonic stem cell:	n/a	chr2:182548851-182548863 chr2:182548850-182548865
2	CTCF	chr2:182548640-182548790	HEK293	kidney:	n/a	n/a
3	CTCF	chr2:182548660-182548810	HRE	kidney:	n/a	n/a
4	CTCF	chr2:182548540-182548690	WERI-Rb-1	eye:	n/a	n/a
5	CTCF	chr2:182548620-182548770	SK-N-SH_RA	brain:	n/a	n/a
6	CHD2	chr2:182548643-182548843	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr2:182548391-182549127	H1-hESC	embryonic stem cell:	n/a	chr2:182549079-182549093
8	ZNF143	chr2:182548032-182549133	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:182547954-182549399	H1-neurons	neurons:	n/a	n/a
10	CTCF	chr2:182548540-182548690	HBMEC	blood vessel:	n/a	n/a
11	MAX	chr2:182548077-182548879	H1-hESC	embryonic stem cell:	n/a	chr2:182548304-182548320
12	POLR2A	chr2:182548121-182549143	H1-neurons	neurons:	n/a	n/a
13	SUZ12	chr2:182546965-182550375	H1-hESC	embryonic stem cell:	n/a	n/a
14	SUZ12	chr2:182543491-182550280	NT2-D1	testis:	n/a	n/a
15	MAX	chr2:182548110-182548846	H1-hESC	embryonic stem cell:	n/a	chr2:182548304-182548320
16	TCF12	chr2:182548548-182548749	H1-hESC	embryonic stem cell:	n/a	n/a
17	TCF12	chr2:182548129-182548872	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F6	chr2:182548087-182548991	H1-hESC	embryonic stem cell:	n/a	chr2:182548851-182548863 chr2:182548850-182548865
19	SIN3A	chr2:182548153-182549051	H1-hESC	embryonic stem cell:	n/a	chr2:182548855-182548866
20	CTBP2	chr2:182547074-182549554	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:182546719..182548427-chr2:182548447..182551068,2	K562	blood:
2	chr2:182542601..182545361-chr2:182546496..182548838,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA4-1	chr2:182546597-182554169	NONHSAT075881

Variant related genes	Relation type
NEUROD1	TF binding region
CERKL	TF binding region
ENSG00000162992	Chromatin interaction
ENSG00000234595	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10178686	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12052558	0.82[ASN][1000 genomes]
rs12053195	0.91[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.82[ASN][1000 genomes]
rs16867465	0.91[CEU][hapmap]
rs16867467	0.91[CEU][hapmap];0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs2696344	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2696345	0.85[YRI][hapmap]
rs2696348	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2696352	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28416292	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28874657	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3755022	0.80[ASN][1000 genomes]
rs3916026	1.00[JPT][hapmap]
rs4666572	0.84[CHB][hapmap]
rs6713027	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6756950	1.00[CEU][hapmap];0.89[CHB][hapmap];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	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
3	nsv834477	chr2:182438121-182593527	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182543600-182550200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr2:182545200-182549000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr2:182545200-182549800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:182545200-182550000	Bivalent Enhancer	Fetal Thymus	thymus
5	chr2:182545200-182550200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:182545200-182550400	Bivalent Enhancer	Fetal Brain Male	brain
7	chr2:182545400-182549400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:182545800-182549400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr2:182546000-182550200	Weak transcription	Gastric	stomach
10	chr2:182547000-182550200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr2:182547200-182549000	Bivalent Enhancer	Spleen	Spleen
12	chr2:182547200-182549400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr2:182547400-182548800	Bivalent Enhancer	Liver	Liver
14	chr2:182547400-182550200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr2:182547400-182550400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
16	chr2:182547400-182550400	Bivalent Enhancer	Placenta	Placenta
17	chr2:182547600-182549000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:182547600-182549200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr2:182547600-182549200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:182547600-182549800	Bivalent Enhancer	Lung	lung
21	chr2:182547600-182550200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:182547800-182548800	Bivalent Enhancer	Psoas Muscle	Psoas
23	chr2:182547800-182548800	Bivalent/Poised TSS	HSMM	muscle
24	chr2:182547800-182549000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
25	chr2:182547800-182549000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
26	chr2:182547800-182549000	Bivalent Enhancer	Left Ventricle	heart
27	chr2:182547800-182549200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr2:182547800-182549200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:182547800-182549200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:182547800-182549200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:182547800-182549200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr2:182547800-182549200	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr2:182547800-182549400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:182547800-182549400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr2:182547800-182549600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
36	chr2:182547800-182549600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr2:182548000-182548800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:182548000-182548800	Bivalent Enhancer	Small Intestine	intestine
39	chr2:182548000-182549200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:182548000-182549400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr2:182548000-182549600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr2:182548000-182550200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
43	chr2:182548200-182548800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:182548200-182548800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:182548200-182548800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:182548200-182548800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
47	chr2:182548200-182548800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
48	chr2:182548200-182548800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
49	chr2:182548200-182548800	Bivalent/Poised TSS	A549	lung
50	chr2:182548200-182548800	Bivalent Enhancer	NHLF	lung

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