Variant report

Variant	rs2190424
Chromosome Location	chr7:86841971-86841972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:86783605..86785196-chr7:86839516..86842290,2	K562	blood:
2	chr7:86790377..86794214-chr7:86840091..86844543,5	K562	blood:
3	chr7:86783605..86785152-chr7:86840790..86843354,2	K562	blood:

Variant related genes	Relation type
ENSG00000135164	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10085726	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10228392	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10231010	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10238917	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10244350	0.89[CEU][hapmap]
rs1024457	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[EUR][1000 genomes]
rs10245036	0.86[GIH][hapmap]
rs10257953	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10273853	0.90[CEU][hapmap]
rs1058972	0.82[GIH][hapmap]
rs10952896	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1859124	0.80[CEU][hapmap]
rs2057984	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs2074757	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2108271	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2108272	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286268	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373387	1.00[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2373388	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs3747807	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789251	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789252	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4140847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4400318	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4639442	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4727146	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4728686	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4728689	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4728690	0.92[GIH][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes]
rs6465093	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs6465101	0.96[EUR][1000 genomes]
rs6952384	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6966613	0.92[AMR][1000 genomes]
rs6968640	0.90[CEU][hapmap]
rs6975202	0.96[EUR][1000 genomes]
rs757961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs765968	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7780698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7800541	0.82[GIH][hapmap]
rs7810647	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs886787	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1016761	chr7:86758544-86914152	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv888676	chr7:86781423-86858824	Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv1026193	chr7:86790391-86856448	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv539003	chr7:86790391-86856448	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
10	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2190424	C7orf23	cis	parietal	SCAN
rs2190424	C7orf23	cis	cerebellum	SCAN
rs2190424	SLC25A40	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86821000-86847400	Weak transcription	Stomach Mucosa	stomach
2	chr7:86825600-86847400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:86825800-86843600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:86826800-86846000	Weak transcription	Fetal Kidney	kidney
5	chr7:86826800-86848200	Weak transcription	Left Ventricle	heart
6	chr7:86828400-86848200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:86829800-86848000	Weak transcription	Right Ventricle	heart
8	chr7:86831000-86847200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:86832000-86843400	Weak transcription	NHLF	lung
10	chr7:86832200-86843200	Weak transcription	Osteobl	bone
11	chr7:86832200-86846000	Weak transcription	HSMM	muscle
12	chr7:86832400-86845600	Weak transcription	Pancreas	Pancrea
13	chr7:86832400-86847200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:86834600-86847200	Weak transcription	Colonic Mucosa	Colon
15	chr7:86834600-86847400	Weak transcription	Esophagus	oesophagus
16	chr7:86834600-86848200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:86835200-86842400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:86835800-86846000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:86836000-86842000	Weak transcription	Brain Anterior Caudate	brain
20	chr7:86836000-86842200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:86836000-86846200	Weak transcription	Fetal Intestine Large	intestine
22	chr7:86836000-86846600	Weak transcription	Hela-S3	cervix
23	chr7:86836200-86842600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:86836200-86845200	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr7:86836200-86847400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr7:86836400-86843400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:86836400-86843400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:86836400-86843600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:86836400-86846000	Weak transcription	Aorta	Aorta
30	chr7:86836400-86846200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:86836400-86846600	Weak transcription	HUVEC	blood vessel
32	chr7:86836400-86848000	Weak transcription	A549	lung
33	chr7:86836600-86846000	Weak transcription	HepG2	liver
34	chr7:86836600-86847800	Weak transcription	NH-A	brain
35	chr7:86836800-86842200	Weak transcription	Brain Hippocampus Middle	brain
36	chr7:86836800-86843400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:86837400-86842200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:86837400-86842200	Weak transcription	Fetal Lung	lung
39	chr7:86837400-86847800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:86837400-86848200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr7:86837400-86848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr7:86838000-86843600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr7:86838200-86847800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr7:86838400-86842200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr7:86838400-86842600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:86838400-86843400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr7:86838400-86848000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr7:86839000-86846000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:86839200-86848000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr7:86839400-86842400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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