Variant report

Variant	rs1344590
Chromosome Location	chr2:173771316-173771317
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173761351..173763071-chr2:173771156..173774150,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLX2-12	chr2:173770689-173771798	refGeneNc_3635_NR_033882

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1469214	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1863174	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1968290	0.84[AMR][1000 genomes]
rs2194723	1.00[YRI][hapmap]
rs2553010	0.84[AMR][1000 genomes]
rs2553012	0.84[AMR][1000 genomes]
rs2553014	0.84[AMR][1000 genomes]
rs2553016	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2553017	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2676514	0.82[AMR][1000 genomes]
rs2676519	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2676527	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4541226	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4972866	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6754271	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7607344	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs933785	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173764400-173792600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:173764800-173776000	Weak transcription	Spleen	Spleen
3	chr2:173767000-173776600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:173769200-173771600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:173769200-173792400	Weak transcription	Fetal Kidney	kidney
6	chr2:173769800-173771600	Enhancers	Fetal Heart	heart
7	chr2:173770400-173771400	Enhancers	Rectal Smooth Muscle	rectum
8	chr2:173770400-173771600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:173770400-173771600	Enhancers	Colon Smooth Muscle	Colon
10	chr2:173770600-173771400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:173770600-173771600	Enhancers	Adipose Nuclei	Adipose
12	chr2:173770600-173771800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr2:173770600-173771800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:173770800-173771400	Enhancers	Brain Angular Gyrus	brain
15	chr2:173770800-173771600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr2:173770800-173771800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr2:173770800-173772000	Enhancers	Left Ventricle	heart
18	chr2:173771000-173771400	Enhancers	Brain Anterior Caudate	brain
19	chr2:173771000-173771400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr2:173771000-173771600	Enhancers	H9 Cell Line	embryonic stem cell
21	chr2:173771000-173771600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr2:173771000-173771600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr2:173771000-173771600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:173771000-173771600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:173771000-173771600	Enhancers	Brain Hippocampus Middle	brain
26	chr2:173771000-173771800	Enhancers	Brain Germinal Matrix	brain
27	chr2:173771000-173771800	Enhancers	Fetal Muscle Leg	muscle
28	chr2:173771000-173771800	Enhancers	Lung	lung
29	chr2:173771000-173771800	Enhancers	Right Ventricle	heart
30	chr2:173771000-173771800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:173771000-173772000	Enhancers	Right Atrium	heart
32	chr2:173771200-173771400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:173771200-173771400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:173771200-173771600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:173771200-173771600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:173771200-173771600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:173771200-173771600	Enhancers	Fetal Thymus	thymus
38	chr2:173771200-173771600	Enhancers	Psoas Muscle	Psoas
39	chr2:173771200-173771800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr2:173771200-173771800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:173771200-173771800	Enhancers	Fetal Muscle Trunk	muscle

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