Variant report

Variant	rs13000846
Chromosome Location	chr2:172181222-172181223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172178792..172182070-chr2:172182308..172185884,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10454741	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11674632	0.91[ASW][hapmap];0.90[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11677795	0.80[EUR][1000 genomes]
rs11679835	0.90[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs11687454	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11691073	0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11694321	0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs11893310	0.80[EUR][1000 genomes]
rs11902733	0.81[EUR][1000 genomes]
rs12105780	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12989392	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12989938	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12995219	0.84[AMR][1000 genomes]
rs12998320	0.96[GIH][hapmap]
rs13002817	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13002867	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13003130	0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13005615	0.87[EUR][1000 genomes]
rs13023287	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13023973	0.93[GIH][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13031794	0.91[ASW][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13398989	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2111459	0.93[GIH][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2356707	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34096402	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34787101	0.83[EUR][1000 genomes]
rs36140780	0.80[EUR][1000 genomes]
rs6722670	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7592018	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13000846	CDCA7	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172163800-172181400	Weak transcription	Gastric	stomach
2	chr2:172169200-172182400	Weak transcription	Aorta	Aorta
3	chr2:172169200-172193400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:172169800-172183200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:172170200-172192800	Weak transcription	Fetal Intestine Large	intestine
6	chr2:172171400-172190800	Weak transcription	Esophagus	oesophagus
7	chr2:172171800-172211600	Weak transcription	Fetal Intestine Small	intestine
8	chr2:172172600-172190600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:172172800-172190600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:172173000-172182200	Weak transcription	Liver	Liver
12	chr2:172173600-172186000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:172175200-172181800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:172175400-172183000	Weak transcription	Fetal Lung	lung
15	chr2:172175400-172187600	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:172175600-172188000	Weak transcription	Adipose Nuclei	Adipose
17	chr2:172175800-172183600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:172176000-172183400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:172176000-172184400	Weak transcription	NHDF-Ad	bronchial
20	chr2:172176000-172187800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:172176200-172181800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:172176200-172182400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:172176200-172183200	Weak transcription	Fetal Stomach	stomach
24	chr2:172176200-172183600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:172176200-172183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:172176200-172198600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:172176400-172183000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:172176400-172183400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:172176600-172182000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:172177000-172182000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:172177000-172183400	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:172177200-172183200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr2:172177400-172182200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:172177400-172183000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:172177400-172183600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:172177600-172184400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:172177800-172182800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:172177800-172183400	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:172178000-172181800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr2:172178000-172182000	Strong transcription	Dnd41	blood
41	chr2:172178000-172183600	Weak transcription	Fetal Brain Male	brain
42	chr2:172178000-172190600	Weak transcription	Left Ventricle	heart
43	chr2:172178400-172182800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:172178400-172183800	Weak transcription	Fetal Kidney	kidney
45	chr2:172178800-172181800	Enhancers	Primary hematopoietic stem cells	blood
46	chr2:172179800-172181800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:172179800-172182000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:172180000-172182400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:172180000-172183600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:172180000-172195800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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