Variant report

Variant	rs34498571
Chromosome Location	chr15:93468550-93468551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93465422..93467834-chr15:93468077..93470952,3	K562	blood:
2	chr15:93461235..93463110-chr15:93467839..93470762,2	K562	blood:
3	chr15:93352951..93354833-chr15:93466989..93469853,2	MCF-7	breast:
4	chr15:93352116..93353918-chr15:93468121..93470710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173575	Chromatin interaction
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10520717	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11632522	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11634204	0.87[AMR][1000 genomes]
rs12901950	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904680	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914508	0.87[AMR][1000 genomes]
rs12915072	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12916015	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28540863	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28668136	0.87[AMR][1000 genomes]
rs34266454	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35327372	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35477598	0.87[AMR][1000 genomes]
rs35596808	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs36048863	0.89[AMR][1000 genomes]
rs4778067	0.81[AMR][1000 genomes]
rs56358327	0.87[AMR][1000 genomes]
rs67190144	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72761955	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	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
8	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
rs34498571	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	chr15:93461200-93471600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:93461600-93471600	Weak transcription	Ovary	ovary
4	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:93462000-93474800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:93463200-93486800	Strong transcription	Dnd41	blood
8	chr15:93463600-93470200	Genic enhancers	Fetal Intestine Large	intestine
9	chr15:93464200-93475000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:93464400-93469600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:93464400-93473600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:93464800-93469200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
13	chr15:93464800-93469600	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr15:93465000-93468600	Genic enhancers	A549	lung
15	chr15:93465000-93471400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:93465400-93468600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:93465400-93469600	Strong transcription	Fetal Stomach	stomach
18	chr15:93465400-93488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:93465600-93468800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:93465600-93469000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:93465600-93469600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:93465600-93472000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:93465800-93468600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:93465800-93469200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr15:93465800-93471600	Weak transcription	Aorta	Aorta
26	chr15:93466000-93469600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:93466000-93471200	Strong transcription	HSMM	muscle
28	chr15:93466000-93471400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:93466000-93473000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr15:93466000-93473600	Strong transcription	Fetal Muscle Leg	muscle
31	chr15:93466000-93476200	Strong transcription	Placenta	Placenta
32	chr15:93466200-93470000	Genic enhancers	GM12878-XiMat	blood
33	chr15:93466200-93470600	Genic enhancers	Duodenum Mucosa	Duodenum
34	chr15:93466200-93471600	Strong transcription	HSMMtube	muscle
35	chr15:93466200-93473200	Strong transcription	Hela-S3	cervix
36	chr15:93466200-93475000	Strong transcription	HUVEC	blood vessel
37	chr15:93466200-93477000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:93466200-93479200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:93466200-93480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr15:93466200-93488200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:93466200-93488200	Strong transcription	Thymus	Thymus
42	chr15:93466200-93489400	Strong transcription	K562	blood
43	chr15:93466400-93471200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:93466400-93471400	Weak transcription	Right Ventricle	heart
45	chr15:93466400-93472200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:93466400-93473200	Strong transcription	NHEK	skin
47	chr15:93466400-93473400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:93466400-93473400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr15:93466400-93475800	Strong transcription	Liver	Liver
50	chr15:93466400-93476400	Weak transcription	Fetal Heart	heart

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