Variant report

Variant	rs10260048
Chromosome Location	chr7:56019694-56019695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:56017138..56022365-chr7:56030961..56033857,7	MCF-7	breast:
2	chr7:56018384..56020889-chr7:56129856..56132224,2	K562	blood:
3	chr7:56018437..56023114-chr7:56029023..56035214,11	K562	blood:
4	chr7:56017145..56021503-chr7:56030472..56033942,8	MCF-7	breast:
5	chr7:56018165..56022272-chr7:56129856..56132253,4	K562	blood:

Variant related genes	Relation type
ENSG00000146729	Chromatin interaction
ENSG00000146731	Chromatin interaction
ENSG00000129103	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10043	0.82[JPT][hapmap]
rs10236322	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260031	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10263766	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11238384	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11238392	0.82[JPT][hapmap]
rs11238393	0.82[JPT][hapmap]
rs11765364	1.00[ASW][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap]
rs11771756	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12538444	0.82[JPT][hapmap]
rs13230292	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13240729	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs15892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967230	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304376	1.00[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2331096	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2331166	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2538048	1.00[ASW][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap]
rs2965455	1.00[ASW][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap]
rs35347591	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4245574	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4540366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4947528	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4947529	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4948083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4948085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4948090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948094	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55634856	0.89[ASN][1000 genomes]
rs56128104	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56207001	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56269128	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56351949	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62456630	0.97[ASN][1000 genomes]
rs62456648	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62456651	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62456653	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62456654	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6421738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6593289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6593290	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6945638	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs6946065	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6965614	1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs6970353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6972415	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6974707	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7790255	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7794115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808729	0.82[JPT][hapmap]
rs816407	1.00[ASW][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs8406	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9649783	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers 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	39 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv981772	chr7:56009678-56020897	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10260048	LOC146325	trans	lymphoblastoid	RTeQTL
rs10260048	CHCHD2	cis	parietal	SCAN
rs10260048	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs10260048	ZNF713	cis	cerebellum	SCAN
rs10260048	CHCHD2	cis	cerebellum	SCAN
rs10260048	CHCHD2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56018400-56020000	Active TSS	Placenta	Placenta
2	chr7:56018400-56020400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr7:56018600-56020600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr7:56018600-56020800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr7:56018800-56019800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr7:56019000-56019800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:56019000-56019800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:56019000-56019800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:56019000-56019800	Active TSS	Brain Angular Gyrus	brain
10	chr7:56019000-56019800	Active TSS	Stomach Smooth Muscle	stomach
11	chr7:56019000-56020000	Active TSS	Primary T cells from cord blood	blood
12	chr7:56019000-56020000	Active TSS	Brain Anterior Caudate	brain
13	chr7:56019000-56020000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr7:56019000-56020000	Active TSS	Esophagus	oesophagus
15	chr7:56019000-56020000	Active TSS	Fetal Brain Female	brain
16	chr7:56019000-56020000	Active TSS	Fetal Muscle Leg	muscle
17	chr7:56019000-56020000	Active TSS	Thymus	Thymus
18	chr7:56019000-56020200	Active TSS	Brain Germinal Matrix	brain
19	chr7:56019000-56020200	Active TSS	Psoas Muscle	Psoas
20	chr7:56019000-56020200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr7:56019000-56020400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:56019000-56020400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:56019000-56020400	Active TSS	Duodenum Mucosa	Duodenum
24	chr7:56019000-56020400	Active TSS	Fetal Intestine Small	intestine
25	chr7:56019000-56020400	Active TSS	Fetal Kidney	kidney
26	chr7:56019000-56020400	Active TSS	Rectal Smooth Muscle	rectum
27	chr7:56019000-56020400	Active TSS	A549	lung
28	chr7:56019000-56020400	Active TSS	Monocytes-CD14+_RO01746	blood
29	chr7:56019000-56020600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:56019000-56020600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:56019000-56020800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr7:56019000-56020800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:56019200-56019800	Active TSS	Primary monocytes fromperipheralblood	blood
34	chr7:56019200-56019800	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr7:56019200-56019800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:56019200-56019800	Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr7:56019200-56019800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr7:56019200-56019800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr7:56019200-56020000	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr7:56019200-56020000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:56019200-56020000	Active TSS	Brain Substantia Nigra	brain
42	chr7:56019200-56020000	Active TSS	Colonic Mucosa	Colon
43	chr7:56019200-56020000	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr7:56019200-56020000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr7:56019200-56020000	Active TSS	Fetal Stomach	stomach
46	chr7:56019200-56020000	Active TSS	Fetal Thymus	thymus
47	chr7:56019200-56020000	Active TSS	Pancreas	Pancrea
48	chr7:56019200-56020000	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr7:56019200-56020200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:56019200-56020200	Active TSS	Muscle Satellite Cultured Cells	--

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