Variant report

Variant	rs7168780
Chromosome Location	chr15:93476350-93476351
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93424935..93427296-chr15:93474407..93476549,3	MCF-7	breast:
2	chr15:93443447..93445715-chr15:93476251..93477957,2	MCF-7	breast:
3	chr15:93474975..93479268-chr15:93480596..93484634,5	K562	blood:
4	chr15:93345609..93348948-chr15:93474005..93477394,3	K562	blood:

Variant related genes	Relation type
ENSG00000272888	Chromatin interaction
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10520716	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11634566	0.85[EUR][1000 genomes]
rs12437674	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438635	0.85[EUR][1000 genomes]
rs12443243	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12594991	0.87[EUR][1000 genomes]
rs12908494	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1318689	0.86[ASN][1000 genomes]
rs1320819	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1406714	0.81[ASN][1000 genomes]
rs1881835	0.93[EUR][1000 genomes]
rs28573213	0.83[ASN][1000 genomes]
rs35865218	0.83[ASN][1000 genomes]
rs3743469	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3826035	0.83[EUR][1000 genomes]
rs3826036	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4327000	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6497009	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6497010	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7164668	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7167194	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7171151	0.92[EUR][1000 genomes]
rs7173103	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7175134	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8024528	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8026695	0.83[ASN][1000 genomes]
rs8035739	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs961233	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
3	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
4	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7168780	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:93463200-93486800	Strong transcription	Dnd41	blood
5	chr15:93465400-93488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:93466200-93477000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:93466200-93479200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr15:93466200-93480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:93466200-93488200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:93466200-93488200	Strong transcription	Thymus	Thymus
11	chr15:93466200-93489400	Strong transcription	K562	blood
12	chr15:93466400-93476400	Weak transcription	Fetal Heart	heart
13	chr15:93466400-93476800	Strong transcription	Primary hematopoietic stem cells	blood
14	chr15:93466400-93480800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:93466400-93489000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:93466600-93476400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:93466600-93490600	Strong transcription	Fetal Lung	lung
18	chr15:93466800-93479600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr15:93466800-93490200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:93467200-93490200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:93467200-93490600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:93467400-93476400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:93467400-93477000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr15:93467400-93489200	Strong transcription	Primary B cells from cord blood	blood
25	chr15:93467400-93490000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr15:93467600-93490400	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr15:93467600-93490600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:93467800-93478600	Strong transcription	Primary T cells from cord blood	blood
29	chr15:93467800-93480000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:93468600-93490400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:93469000-93489800	Strong transcription	Fetal Thymus	thymus
32	chr15:93469600-93484600	Strong transcription	Left Ventricle	heart
33	chr15:93470000-93479800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:93470000-93488200	Strong transcription	GM12878-XiMat	blood
35	chr15:93470200-93476600	Strong transcription	Fetal Intestine Large	intestine
36	chr15:93470200-93476800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr15:93470600-93476400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr15:93470600-93476600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr15:93470600-93476600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr15:93471200-93478800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:93471400-93477000	Strong transcription	Brain Germinal Matrix	brain
42	chr15:93472400-93478000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:93472400-93478600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:93472400-93478800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:93472600-93476400	Weak transcription	Stomach Mucosa	stomach
46	chr15:93472600-93477000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr15:93472600-93478600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:93473400-93476800	Strong transcription	Fetal Intestine Small	intestine
49	chr15:93473400-93480200	Strong transcription	Fetal Brain Female	brain
50	chr15:93473600-93479200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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