Variant report

Variant	rs7222403
Chromosome Location	chr17:19879164-19879165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:19877195..19879459-chr17:19883535..19885344,2	K562	blood:
2	chr17:19769754..19773058-chr17:19878983..19882883,4	MCF-7	breast:
3	chr17:19879148..19882537-chr17:19911149..19913260,3	MCF-7	breast:
4	chr17:19864763..19867496-chr17:19878736..19880749,2	K562	blood:
5	chr17:19873620..19876198-chr17:19879057..19880667,2	MCF-7	breast:
6	chr17:19878871..19883594-chr17:20057277..20060362,4	K562	blood:
7	chr17:19877816..19880542-chr17:20058157..20059665,2	MCF-7	breast:
8	chr17:19875702..19877605-chr17:19877615..19879225,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction
ENSG00000128487	Chromatin interaction
ENSG00000261033	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11204419	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204420	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204421	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs119672	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1479129	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1638525	0.93[CEU][hapmap];0.93[CHB][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1638526	0.83[YRI][hapmap]
rs169412	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169414	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175921	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs175922	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1860302	0.94[CHB][hapmap]
rs191865	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203450	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203451	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203452	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203455	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs203456	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203457	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203458	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203459	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203460	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203461	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203462	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203465	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203466	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203469	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs203470	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203477	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203479	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203481	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203482	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2108978	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35003563	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs397969	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4479308	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4924803	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs4925060	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925065	0.94[CHB][hapmap]
rs4925072	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs4925077	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs4925081	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs56153261	0.84[ASN][1000 genomes]
rs6587206	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207625	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs7208025	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7208365	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7209734	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs8066150	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs850623	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860335	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs888423	0.94[CHB][hapmap]
rs918227	0.87[CHB][hapmap]
rs9906625	0.81[AFR][1000 genomes]
rs9907752	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9914273	0.91[CEU][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs9916675	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7222403	AKAP10	cis	normal skin	skin_eQTL
rs7222403	AKAP10	cis	uninvolved skin	skin_eQTL
rs7222403	AKAP10	cis	lesional skin	skin_eQTL
rs7222403	AKAP10	cis	Lymphoblastoid	GTEx
rs7222403	AKAP10	cis	multi-tissue	Pritchard
rs7222403	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
2	chr17:19850600-19879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:19850600-19880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:19850600-19880200	Weak transcription	Aorta	Aorta
5	chr17:19852200-19879400	Weak transcription	Esophagus	oesophagus
6	chr17:19852200-19879600	Weak transcription	Right Ventricle	heart
7	chr17:19852200-19880000	Weak transcription	Psoas Muscle	Psoas
8	chr17:19857400-19880400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:19857600-19880200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:19859800-19879400	Weak transcription	Brain Angular Gyrus	brain
11	chr17:19861800-19880000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr17:19862000-19879200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr17:19862000-19880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr17:19862000-19880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr17:19862200-19880000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr17:19863400-19879600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:19863600-19879800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:19865000-19879600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr17:19865200-19880200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr17:19866400-19879400	Weak transcription	Spleen	Spleen
21	chr17:19869000-19880200	Weak transcription	HSMMtube	muscle
22	chr17:19869200-19879400	Weak transcription	Stomach Mucosa	stomach
23	chr17:19870200-19880000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr17:19872000-19880000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr17:19872000-19880200	Weak transcription	Colonic Mucosa	Colon
26	chr17:19872600-19879200	Weak transcription	Osteobl	bone
27	chr17:19872600-19879400	Weak transcription	Left Ventricle	heart
28	chr17:19872600-19879600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:19872600-19880000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr17:19872800-19879400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:19872800-19879600	Weak transcription	Lung	lung
32	chr17:19873000-19879200	Weak transcription	HMEC	breast
33	chr17:19873400-19879200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:19873600-19879200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:19873600-19879200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr17:19873600-19879400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr17:19873600-19879800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr17:19873600-19880000	Weak transcription	NHDF-Ad	bronchial
39	chr17:19873800-19879200	Weak transcription	K562	blood
40	chr17:19874000-19879400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr17:19874000-19879400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr17:19874200-19880000	Weak transcription	Fetal Muscle Leg	muscle
43	chr17:19874400-19879400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr17:19874400-19880400	Weak transcription	Ovary	ovary
45	chr17:19874600-19879200	Weak transcription	Brain Germinal Matrix	brain
46	chr17:19874600-19879400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr17:19874600-19879400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr17:19874600-19880000	Weak transcription	HUVEC	blood vessel
49	chr17:19874600-19880000	Weak transcription	NHEK	skin
50	chr17:19874600-19880600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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