Variant report

Variant	rs7435601
Chromosome Location	chr4:3369645-3369646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3368401..3370679-chr4:3386543..3390085,3	MCF-7	breast:
2	chr4:3367776..3369729-chr4:3369770..3372285,2	K562	blood:
3	chr4:3368324..3371112-chr4:3371223..3374209,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10155132	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10937924	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13104157	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13150241	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17805201	1.00[YRI][hapmap]
rs2051558	0.90[JPT][hapmap]
rs2236052	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2239725	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2699433	1.00[YRI][hapmap]
rs2748447	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2749778	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2749780	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2749781	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2749782	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2749783	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2749785	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2798221	0.80[CHB][hapmap]
rs2857982	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129308	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs3129310	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs3129327	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129328	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3129334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3135145	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3135146	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60181496	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60208975	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6819202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs881817	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs910568	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised 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	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3441228	chr4:3367804-3370302	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3339213	chr4:3368054-3372352	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7435601	DGKQ	cis	parietal	SCAN
rs7435601	RGS12	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3334000-3370600	Weak transcription	Right Atrium	heart
2	chr4:3360400-3370000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr4:3360600-3370000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr4:3361400-3370000	Weak transcription	HSMM	muscle
5	chr4:3363600-3371000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:3364800-3370400	Weak transcription	Pancreas	Pancrea
7	chr4:3364800-3370400	Weak transcription	NHLF	lung
8	chr4:3364800-3370600	Weak transcription	Esophagus	oesophagus
9	chr4:3365000-3371000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:3365600-3370400	Weak transcription	Gastric	stomach
11	chr4:3365800-3370000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:3365800-3370000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:3366000-3370200	Weak transcription	Primary T cells from cord blood	blood
14	chr4:3366000-3370400	Weak transcription	Thymus	Thymus
15	chr4:3366000-3370600	Weak transcription	Colonic Mucosa	Colon
16	chr4:3366400-3369800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:3366400-3370000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:3366400-3370200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:3366400-3370400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:3366400-3370600	Weak transcription	Adipose Nuclei	Adipose
21	chr4:3366600-3370000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:3366600-3370600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:3366800-3370600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:3366800-3372200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr4:3367000-3370000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:3367000-3370000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:3367000-3371200	Enhancers	Fetal Brain Male	brain
28	chr4:3367200-3370400	Weak transcription	Brain Anterior Caudate	brain
29	chr4:3367400-3371000	Weak transcription	Fetal Kidney	kidney
30	chr4:3367400-3371400	Enhancers	Fetal Muscle Leg	muscle
31	chr4:3367600-3370600	Enhancers	Fetal Brain Female	brain
32	chr4:3368000-3370000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:3368000-3370000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:3368000-3370000	Weak transcription	Right Ventricle	heart
35	chr4:3368000-3371400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:3368000-3373800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:3368200-3371200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr4:3368400-3370000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:3368400-3371000	Weak transcription	Ovary	ovary
40	chr4:3368400-3371400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:3368800-3371000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:3368800-3372400	Enhancers	Lung	lung
43	chr4:3368800-3376800	Enhancers	Spleen	Spleen
44	chr4:3369000-3370200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:3369000-3370400	Weak transcription	Placenta	Placenta
46	chr4:3369000-3370600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:3369000-3370800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr4:3369000-3370800	Weak transcription	Fetal Intestine Large	intestine
49	chr4:3369000-3371000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:3369000-3371200	Enhancers	Fetal Heart	heart

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