Variant report

Variant	rs3779518
Chromosome Location	chr7:103847248-103847249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:103846497..103848385-chr7:103909952..103912269,2	MCF-7	breast:
2	chr7:103628555..103630772-chr7:103847007..103849982,2	K562	blood:
3	chr7:103846124..103848372-chr7:103861589..103863576,2	MCF-7	breast:
4	chr7:103835421..103837340-chr7:103844960..103847432,2	K562	blood:
5	chr7:103847011..103848620-chr7:142657967..142659467,2	MCF-7	breast:
6	chr7:103833753..103835540-chr7:103846175..103847854,2	K562	blood:

Variant related genes	Relation type
ENSG00000197993	Chromatin interaction
ENSG00000189056	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10251561	0.82[LWK][hapmap]
rs10263828	0.83[YRI][hapmap]
rs1035169	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10808128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953408	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs113877	0.84[ASN][1000 genomes]
rs12056186	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12056191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12112576	0.82[YRI][hapmap]
rs12705180	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12705181	0.95[ASN][1000 genomes]
rs12705184	0.81[ASN][1000 genomes]
rs12705187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12705188	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs12705190	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12705191	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs12705192	0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs12705193	0.93[EUR][1000 genomes]
rs12705195	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230700	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs13238183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs193888	0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs194837	0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs194838	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs194840	0.82[YRI][hapmap]
rs194841	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs194846	0.85[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs194847	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs194849	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs194851	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs194857	0.85[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs194858	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs194859	0.84[ASN][1000 genomes]
rs194861	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs194865	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs194867	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs194868	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2160397	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245659	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2283035	0.93[EUR][1000 genomes]
rs2299408	0.85[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs2299409	0.88[ASN][1000 genomes]
rs2299411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307409	0.82[YRI][hapmap]
rs2385140	0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs34096272	0.91[EUR][1000 genomes]
rs35034355	1.00[ASN][1000 genomes]
rs3757734	0.96[ASN][1000 genomes]
rs3808008	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3808009	0.83[ASN][1000 genomes]
rs3808010	0.84[ASN][1000 genomes]
rs3823979	0.84[ASN][1000 genomes]
rs4140860	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4265123	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4265124	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4385404	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4461830	0.92[ASN][1000 genomes]
rs62485910	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6948583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961262	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6967757	0.95[ASN][1000 genomes]
rs765408	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7781828	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019640	chr7:103813522-103884705	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv1026481	chr7:103813522-103890770	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	esv2762692	chr7:103813522-103890782	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv526062	chr7:103817597-103891085	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv608065	chr7:103817597-103990755	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3779518	ZNHIT1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103839800-103847400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:103840000-103847600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:103840400-103847800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:103840600-103847800	Weak transcription	Small Intestine	intestine
5	chr7:103842400-103847400	Weak transcription	Lung	lung
6	chr7:103843800-103847600	Weak transcription	Aorta	Aorta
7	chr7:103844000-103847600	Weak transcription	Gastric	stomach
8	chr7:103844200-103847400	Weak transcription	Esophagus	oesophagus
9	chr7:103844200-103847400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr7:103844200-103847400	Weak transcription	Fetal Muscle Leg	muscle
11	chr7:103844200-103847400	Weak transcription	Placenta	Placenta
12	chr7:103844200-103847600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:103844400-103847400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:103844800-103847400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr7:103846000-103847400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:103846000-103847400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:103846200-103847400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:103846200-103847400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr7:103846200-103847600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:103846200-103847600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:103846200-103847600	Flanking Active TSS	Dnd41	blood
22	chr7:103846200-103847800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:103846200-103847800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr7:103846200-103847800	Enhancers	Spleen	Spleen
25	chr7:103846200-103849200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:103846200-103849400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:103846400-103847400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr7:103846400-103847400	Flanking Active TSS	HepG2	liver
29	chr7:103846400-103847800	Flanking Active TSS	Liver	Liver
30	chr7:103846400-103849400	Active TSS	A549	lung
31	chr7:103846600-103848000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:103846600-103849000	Active TSS	K562	blood
33	chr7:103846600-103849400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr7:103846800-103847400	Enhancers	Colonic Mucosa	Colon
35	chr7:103846800-103847400	Enhancers	Fetal Intestine Small	intestine
36	chr7:103846800-103847400	Enhancers	Thymus	Thymus
37	chr7:103846800-103847600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr7:103846800-103847600	Enhancers	Primary B cells from peripheral blood	blood
39	chr7:103846800-103847600	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr7:103846800-103847600	Flanking Active TSS	Hela-S3	cervix
41	chr7:103846800-103847600	Flanking Active TSS	HMEC	breast
42	chr7:103846800-103847800	Flanking Active TSS	NHEK	skin
43	chr7:103846800-103848000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:103846800-103848200	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr7:103846800-103849200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:103847000-103847400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr7:103847000-103847400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr7:103847000-103847400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr7:103847000-103847600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr7:103847000-103847600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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