Variant report

Variant	rs10015979
Chromosome Location	chr4:3109442-3109443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3073984..3078977-chr4:3107018..3111318,5	MCF-7	breast:
2	chr4:3108752..3110861-chr4:3116239..3118784,2	MCF-7	breast:
3	chr4:3108596..3110379-chr4:3112346..3116556,3	K562	blood:
4	chr4:3108607..3111576-chr4:3111924..3115873,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251075	Chromatin interaction
ENSG00000197386	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11731237	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2298969	0.80[ASN][1000 genomes]
rs28820097	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs363096	0.89[GIH][hapmap]
rs71597207	0.83[ASN][1000 genomes]
rs762855	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]

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	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	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10015979	TACC3	cis	parietal	SCAN
rs10015979	TMEM128	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3078200-3109800	Weak transcription	Stomach Mucosa	stomach
2	chr4:3078600-3113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:3080000-3117800	Weak transcription	Small Intestine	intestine
4	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:3094400-3123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:3097200-3143400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:3098600-3109800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:3099800-3114400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:3100000-3110400	Strong transcription	Primary hematopoietic stem cells	blood
13	chr4:3100000-3159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:3100400-3112000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:3101000-3111800	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:3101000-3113000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:3101000-3113800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:3101000-3120600	Strong transcription	Fetal Stomach	stomach
19	chr4:3101000-3122600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:3101000-3124200	Strong transcription	Fetal Intestine Large	intestine
21	chr4:3101000-3124400	Strong transcription	Thymus	Thymus
22	chr4:3101600-3124200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:3101800-3114400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:3104800-3115200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:3105400-3123800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:3105400-3124800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:3105800-3110400	Strong transcription	Spleen	Spleen
28	chr4:3105800-3113200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:3105800-3115400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr4:3105800-3121400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:3106200-3111000	Strong transcription	Lung	lung
32	chr4:3106200-3113400	Strong transcription	Fetal Muscle Leg	muscle
33	chr4:3106400-3111800	Strong transcription	Brain Germinal Matrix	brain
34	chr4:3106400-3112400	Strong transcription	Brain Angular Gyrus	brain
35	chr4:3106400-3115400	Strong transcription	Fetal Lung	lung
36	chr4:3106400-3123400	Strong transcription	Primary T cells from cord blood	blood
37	chr4:3106400-3123800	Strong transcription	Fetal Thymus	thymus
38	chr4:3106400-3145000	Strong transcription	Dnd41	blood
39	chr4:3106600-3115600	Strong transcription	Fetal Brain Female	brain
40	chr4:3106800-3125200	Strong transcription	Primary B cells from cord blood	blood
41	chr4:3107000-3114200	Strong transcription	HepG2	liver
42	chr4:3107600-3110200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:3107800-3109800	Genic enhancers	Stomach Smooth Muscle	stomach
44	chr4:3108000-3113200	Weak transcription	Gastric	stomach
45	chr4:3108200-3109600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr4:3108200-3109800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:3108200-3110400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:3108200-3110400	Enhancers	Adipose Nuclei	Adipose
49	chr4:3108200-3110400	Genic enhancers	Brain Anterior Caudate	brain
50	chr4:3108200-3110800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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