Variant report

Variant	rs7972413
Chromosome Location	chr12:124108296-124108297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124103214..124105859-chr12:124106055..124109639,4	MCF-7	breast:
2	chr12:124107277..124111165-chr12:124113286..124117641,5	MCF-7	breast:
3	chr12:124107998..124110847-chr12:124196796..124199749,2	MCF-7	breast:
4	chr12:124105734..124108451-chr12:124133249..124135719,2	K562	blood:

Variant related genes	Relation type
ENSG00000185344	Chromatin interaction
ENSG00000111361	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10846535	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11057307	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11057320	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1515814	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3748269	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4040225	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4456350	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6488883	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6551	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7134896	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7135624	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7302183	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7313628	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786422	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs786423	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs786425	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs786441	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs786443	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs786444	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs786445	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs786447	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs786448	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs786449	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs786452	0.82[ASN][1000 genomes]
rs7966882	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7971452	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs908373	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1040356	chr12:124094758-124172731	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv3369941	chr12:124108104-124108348	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7972413	TCTN2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124087800-124109600	Weak transcription	Right Atrium	heart
2	chr12:124088200-124116000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:124088200-124117000	Strong transcription	Fetal Stomach	stomach
4	chr12:124088400-124116000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:124088400-124116000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:124088400-124116000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:124088400-124116000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:124088400-124116000	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:124088400-124116200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:124088400-124116800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr12:124088400-124117000	Strong transcription	Fetal Intestine Small	intestine
12	chr12:124088600-124116000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:124088600-124116000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:124088600-124116000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:124088600-124116000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:124088600-124116000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:124088600-124116000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr12:124088600-124116200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:124088600-124116200	Strong transcription	Fetal Thymus	thymus
20	chr12:124088600-124116800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:124088600-124116800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:124088600-124116800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr12:124088600-124117000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr12:124088800-124116000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:124088800-124116000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:124088800-124116000	Strong transcription	Fetal Intestine Large	intestine
27	chr12:124089000-124116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:124089000-124116200	Strong transcription	Brain Germinal Matrix	brain
29	chr12:124089200-124115400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:124089200-124116000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:124089200-124116000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:124089200-124116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:124089200-124116200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:124089200-124116400	Strong transcription	Liver	Liver
35	chr12:124089200-124116600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr12:124089600-124116000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:124089600-124116000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:124089600-124116000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:124089800-124116200	Strong transcription	Thymus	Thymus
40	chr12:124089800-124117000	Strong transcription	Placenta	Placenta
41	chr12:124090000-124115600	Strong transcription	GM12878-XiMat	blood
42	chr12:124090000-124116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:124090000-124116000	Strong transcription	Primary B cells from cord blood	blood
44	chr12:124090000-124116000	Strong transcription	Primary T cells from cord blood	blood
45	chr12:124090200-124116000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:124090200-124116000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr12:124090200-124116000	Strong transcription	Rectal Smooth Muscle	rectum
48	chr12:124090200-124116200	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:124090200-124116200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:124090200-124116200	Strong transcription	Brain Anterior Caudate	brain

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