Variant report

Variant	rs7678305
Chromosome Location	chr4:175236263-175236264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:175236259..175238610-chr5:137804763..137806400,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11929798	0.85[AMR][1000 genomes]
rs11933187	0.85[AMR][1000 genomes]
rs11940726	0.83[AMR][1000 genomes]
rs11940758	0.84[AMR][1000 genomes]
rs11942947	0.87[AMR][1000 genomes]
rs11947136	0.84[AMR][1000 genomes]
rs13101580	0.83[MEX][hapmap];0.86[AMR][1000 genomes]
rs17060455	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs17060459	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs17060468	0.89[JPT][hapmap]
rs34407356	0.85[AMR][1000 genomes]
rs34888351	0.89[AMR][1000 genomes]
rs35332594	0.84[AMR][1000 genomes]
rs4695918	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4695919	0.85[AMR][1000 genomes]
rs4695920	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695921	0.86[AMR][1000 genomes]
rs7685970	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs7699942	0.82[CHD][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7678305	KIAA1712	cis	cerebellum	SCAN
rs7678305	KIAA1712	cis	parietal	SCAN
rs7678305	CEP44	cis	Thyroid	GTEx
rs7678305	KIAA1712	cis	multi-tissue	Pritchard
rs7678305	CEP44	cis	Esophagus Muscularis	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175205600-175241600	Weak transcription	Small Intestine	intestine
2	chr4:175206200-175241000	Weak transcription	Right Ventricle	heart
3	chr4:175206600-175237800	Weak transcription	Osteobl	bone
4	chr4:175206800-175241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:175207000-175239000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:175207000-175240000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:175207000-175242000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:175214200-175239200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:175214600-175237200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:175214600-175237400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:175214600-175238000	Weak transcription	HMEC	breast
12	chr4:175214600-175238400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:175214600-175238800	Weak transcription	Aorta	Aorta
14	chr4:175214600-175239000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:175214600-175239000	Weak transcription	HepG2	liver
16	chr4:175214600-175240000	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:175214600-175240200	Weak transcription	Brain Angular Gyrus	brain
18	chr4:175214600-175240600	Weak transcription	Fetal Stomach	stomach
19	chr4:175214600-175241600	Weak transcription	Lung	lung
20	chr4:175214600-175241600	Weak transcription	Thymus	Thymus
21	chr4:175214600-175241800	Weak transcription	Pancreas	Pancrea
22	chr4:175214600-175242000	Weak transcription	Brain Substantia Nigra	brain
23	chr4:175214600-175243200	Weak transcription	Ovary	ovary
24	chr4:175214600-175244800	Weak transcription	Psoas Muscle	Psoas
25	chr4:175214600-175245400	Weak transcription	HSMM	muscle
26	chr4:175214600-175254800	Weak transcription	Esophagus	oesophagus
27	chr4:175214800-175239200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:175214800-175240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:175214800-175241200	Weak transcription	Brain Anterior Caudate	brain
30	chr4:175215200-175241600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:175215200-175242600	Weak transcription	GM12878-XiMat	blood
32	chr4:175217600-175241600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:175217800-175240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:175218600-175242000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:175219000-175239600	Weak transcription	Fetal Brain Female	brain
36	chr4:175219000-175242800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:175219600-175237800	Weak transcription	HUVEC	blood vessel
38	chr4:175221400-175239200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:175221600-175240600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:175222400-175242000	Weak transcription	Fetal Intestine Small	intestine
41	chr4:175222600-175241400	Weak transcription	Spleen	Spleen
42	chr4:175225000-175237600	Weak transcription	NH-A	brain
43	chr4:175225400-175241800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:175225800-175240800	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:175225800-175241600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:175227400-175238800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:175229000-175237400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:175229200-175238000	Strong transcription	Primary B cells from cord blood	blood
49	chr4:175229600-175237600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:175230000-175245800	Weak transcription	Fetal Muscle Leg	muscle

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