Variant report

Variant	rs4377880
Chromosome Location	chr7:102473163-102473164
allele	A/G
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	EP300	chr7:102472910-102474089	SK-N-SH	brain:	n/a	chr7:102473708-102473722
2	PBX3	chr7:102472907-102474045	SK-N-SH	brain:	n/a	n/a
3	FOXM1	chr7:102472811-102473906	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr7:102473053-102473636	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr7:102472958-102474037	SK-N-SH	brain:	n/a	n/a
6	TAF1	chr7:102473143-102473505	SK-N-SH	brain:	n/a	n/a
7	REST	chr7:102473154-102473467	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr7:102472862-102473896	SK-N-SH	brain:	n/a	n/a
9	TEAD4	chr7:102472939-102473923	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr7:102472871-102474007	SK-N-SH	brain:	n/a	n/a
11	EP300	chr7:102473112-102473892	SK-N-SH_RA	brain:	n/a	chr7:102473708-102473722
12	SIN3AK20	chr7:102473075-102473489	SK-N-SH	brain:	n/a	n/a
13	EP300	chr7:102473031-102473579	SK-N-SH_RA	brain:	n/a	n/a
14	FOSL2	chr7:102472960-102473919	SK-N-SH	brain:	n/a	n/a
15	REST	chr7:102473074-102473474	SK-N-SH	brain:	n/a	n/a
16	PBX3	chr7:102472956-102474011	SK-N-SH	brain:	n/a	n/a
17	RAD21	chr7:102473097-102473517	SK-N-SH_RA	brain:	n/a	n/a
18	RAD21	chr7:102473061-102473439	SK-N-SH_RA	brain:	n/a	n/a
19	GATA3	chr7:102472855-102474062	SK-N-SH	brain:	n/a	n/a
20	TEAD4	chr7:102472904-102473836	SK-N-SH	brain:	n/a	n/a
21	TCF12	chr7:102472835-102474053	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr7:102473037-102473820	SK-N-SH	brain:	n/a	n/a
23	RXRA	chr7:102473077-102473777	SK-N-SH	brain:	n/a	chr7:102473434-102473443
24	EP300	chr7:102472852-102473957	SK-N-SH	brain:	n/a	chr7:102473708-102473722
25	JUND	chr7:102473007-102473959	SK-N-SH	brain:	n/a	n/a
26	EP300	chr7:102472618-102474267	SK-N-SH	brain:	n/a	chr7:102473708-102473722
27	POLR2A	chr7:102473147-102473538	SK-N-SH	brain:	n/a	n/a
28	JUND	chr7:102472964-102474023	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102471265..102473661-chr7:102474795..102476825,2	K562	blood:

Variant related genes	Relation type
RNU6-1136P	TF binding region
ENSG00000252643	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10487281	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10487284	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11496066	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12113073	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12113233	0.82[EUR][1000 genomes]
rs12113759	1.00[CHB][hapmap]
rs17135875	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17135913	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17135916	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17474893	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2041094	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2411061	1.00[CHB][hapmap]
rs3893651	1.00[ASN][1000 genomes]
rs4398822	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4610658	1.00[CHB][hapmap]
rs55681588	1.00[ASN][1000 genomes]
rs55781834	1.00[ASN][1000 genomes]
rs56314487	1.00[ASN][1000 genomes]
rs56692051	1.00[ASN][1000 genomes]
rs6955064	1.00[ASN][1000 genomes]
rs6964296	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6968036	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs727175	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73192015	1.00[ASN][1000 genomes]
rs73192019	1.00[ASN][1000 genomes]
rs7779854	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7781557	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7809047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats 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 miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2761100	chr7:102335787-102481978	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS 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	6 gene(s)	inside rSNPs	diseases
9	nsv608059	chr7:102470455-102504773	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4377880	ZAN	cis	parietal	SCAN
rs4377880	CUX1	cis	cerebellum	SCAN
rs4377880	RELN	cis	cerebellum	SCAN
rs4377880	ACHE	cis	cerebellum	SCAN
rs4377880	DPY19L2P2	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102421600-102475600	Weak transcription	Fetal Thymus	thymus
2	chr7:102422000-102474800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr7:102422000-102476000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr7:102447400-102477200	Weak transcription	Psoas Muscle	Psoas
5	chr7:102448000-102479000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:102450000-102475000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:102450200-102475600	Weak transcription	Esophagus	oesophagus
8	chr7:102452000-102480000	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:102454200-102484600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:102454400-102475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:102454600-102475000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:102454600-102475600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr7:102454800-102473200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:102455000-102475000	Weak transcription	NHLF	lung
15	chr7:102455000-102475000	Weak transcription	Osteobl	bone
16	chr7:102455600-102473200	Weak transcription	HSMM	muscle
17	chr7:102459800-102481800	Weak transcription	Brain Substantia Nigra	brain
18	chr7:102460000-102474800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:102460000-102475000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:102460200-102475200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:102460400-102474600	Weak transcription	HUVEC	blood vessel
22	chr7:102460400-102477000	Weak transcription	Stomach Mucosa	stomach
23	chr7:102460400-102480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:102460800-102480800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:102463200-102475000	Weak transcription	A549	lung
26	chr7:102466200-102473800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr7:102466400-102475000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:102468000-102474600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:102468000-102475000	Weak transcription	HMEC	breast
30	chr7:102468000-102484600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr7:102468200-102481000	Weak transcription	Brain Germinal Matrix	brain
32	chr7:102469000-102473400	Strong transcription	K562	blood
33	chr7:102469800-102477600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr7:102469800-102478400	Weak transcription	Fetal Intestine Small	intestine
35	chr7:102469800-102478800	Weak transcription	Primary B cells from cord blood	blood
36	chr7:102470000-102475600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:102470000-102477600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:102470000-102478000	Weak transcription	HepG2	liver
39	chr7:102470000-102479000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr7:102470000-102490200	Weak transcription	Gastric	stomach
41	chr7:102470000-102516400	Weak transcription	Pancreas	Pancrea
42	chr7:102470200-102474000	Weak transcription	Spleen	Spleen
43	chr7:102470200-102474800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:102470200-102475000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:102470200-102475000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:102470200-102475000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr7:102470200-102476800	Weak transcription	Fetal Heart	heart
48	chr7:102470200-102477000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr7:102470200-102478400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr7:102470200-102481800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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