Variant report

Variant	rs11764629
Chromosome Location	chr7:56155035-56155036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56153997..56155986-chr7:56159698..56162469,2	K562	blood:
2	chr7:56153270..56156192-chr7:56157792..56160758,3	K562	blood:

Variant related genes	Relation type
ENSG00000164776	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10043	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1064337	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11238392	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238393	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238395	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11765364	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772545	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12535749	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12535872	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538444	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894833	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894834	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2002693	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2080141	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538048	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908546	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908547	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908548	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965455	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55697950	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55863006	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56389944	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56401951	0.83[ASN][1000 genomes]
rs62457279	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457281	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457282	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457284	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457286	0.82[ASN][1000 genomes]
rs62457287	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457288	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457289	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457291	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6951202	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955663	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6965614	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73140771	0.86[AMR][1000 genomes]
rs7801405	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7808729	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811889	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs816407	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816410	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8406	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649860	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers 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 target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11764629	LOC146325	trans	lymphoblastoid	RTeQTL
rs11764629	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs11764629	CHCHD2	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
3	chr7:56138800-56156200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:56142000-56168000	Weak transcription	GM12878-XiMat	blood
6	chr7:56142200-56167800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:56142400-56156400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:56142600-56159800	Strong transcription	Fetal Intestine Small	intestine
9	chr7:56144200-56157200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:56146000-56167800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:56146200-56157400	Weak transcription	K562	blood
12	chr7:56147000-56167400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:56147400-56158000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:56147400-56167000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:56147400-56169800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:56147600-56155800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:56147600-56160400	Weak transcription	Fetal Brain Male	brain
18	chr7:56147600-56167200	Weak transcription	HMEC	breast
19	chr7:56147600-56167400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:56147800-56155400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr7:56147800-56157000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:56147800-56159600	Weak transcription	NHDF-Ad	bronchial
23	chr7:56147800-56160200	Weak transcription	HSMM	muscle
24	chr7:56147800-56160600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:56147800-56160800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:56147800-56164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr7:56147800-56167200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr7:56147800-56167400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:56148000-56165600	Weak transcription	Primary B cells from cord blood	blood
30	chr7:56148000-56167200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:56148800-56167400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr7:56149400-56156400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:56149600-56167200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:56149800-56167600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:56149800-56168000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr7:56150000-56155200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:56150000-56164000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:56150000-56166200	Weak transcription	Fetal Thymus	thymus
39	chr7:56150000-56166400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr7:56150200-56160600	Weak transcription	NHEK	skin
41	chr7:56150400-56155400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:56150400-56164000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:56150600-56159600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:56150800-56160400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr7:56151000-56156400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:56151200-56159200	Weak transcription	Fetal Lung	lung
47	chr7:56151400-56157200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr7:56151400-56157200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
49	chr7:56151400-56158200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr7:56151400-56159600	Weak transcription	Brain Angular Gyrus	brain

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