Variant report

Variant	rs1409711
Chromosome Location	chr10:97310431-97310432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:97309672..97311515-chr10:97317695..97319479,2	MCF-7	breast:
2	chr10:97308793..97313420-chr10:97319109..97323255,4	K562	blood:
3	chr10:97299249..97301273-chr10:97310241..97312398,2	K562	blood:

Variant related genes	Relation type
ENSG00000095637	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10736090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786216	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10786220	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10786223	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10786225	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1887227	1.00[ASN][1000 genomes]
rs1926817	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[ASN][1000 genomes]
rs7092277	1.00[ASW][hapmap];1.00[CHD][hapmap]
rs7909386	1.00[ASW][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs943346	1.00[MEX][hapmap];1.00[MKK][hapmap];0.80[EUR][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	esv1808679	chr10:97266478-97316855	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv552022	chr10:97308114-97328227	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1409711	GTSF1	trans	lymphoblastoid	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97296400-97311400	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr10:97296800-97312600	Weak transcription	Placenta	Placenta
3	chr10:97301000-97315200	Enhancers	HepG2	liver
4	chr10:97301800-97311000	Weak transcription	Colonic Mucosa	Colon
5	chr10:97304200-97310800	Enhancers	Rectal Smooth Muscle	rectum
6	chr10:97304600-97312400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:97305000-97311200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr10:97305000-97311400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr10:97305200-97318600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr10:97305200-97319000	Weak transcription	HSMM	muscle
11	chr10:97306600-97311600	Enhancers	Fetal Heart	heart
12	chr10:97306600-97312200	Weak transcription	Fetal Intestine Small	intestine
13	chr10:97306800-97311400	Enhancers	Right Ventricle	heart
14	chr10:97306800-97313000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr10:97307200-97310600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr10:97307400-97310800	Weak transcription	Esophagus	oesophagus
17	chr10:97307800-97310800	Weak transcription	Fetal Intestine Large	intestine
18	chr10:97308000-97311000	Enhancers	Fetal Stomach	stomach
19	chr10:97308000-97318600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:97308600-97311400	Enhancers	Brain Hippocampus Middle	brain
21	chr10:97308600-97311600	Enhancers	Liver	Liver
22	chr10:97309000-97311400	Enhancers	Fetal Muscle Leg	muscle
23	chr10:97309400-97311400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr10:97309400-97311400	Enhancers	Brain Angular Gyrus	brain
25	chr10:97309400-97311400	Enhancers	Left Ventricle	heart
26	chr10:97309400-97311400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr10:97309400-97311600	Enhancers	Brain Substantia Nigra	brain
28	chr10:97309400-97312600	Enhancers	Right Atrium	heart
29	chr10:97309400-97313000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr10:97309600-97310800	Enhancers	Fetal Lung	lung
31	chr10:97309600-97310800	Enhancers	Pancreas	Pancrea
32	chr10:97309600-97311000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
33	chr10:97309600-97311400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr10:97309600-97311400	Enhancers	Brain Anterior Caudate	brain
35	chr10:97309600-97311400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr10:97309600-97311400	Enhancers	K562	blood
37	chr10:97309600-97311800	Enhancers	Stomach Mucosa	stomach
38	chr10:97309600-97312000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:97309600-97312600	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr10:97309600-97312800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr10:97309600-97313000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr10:97309600-97313000	Enhancers	Psoas Muscle	Psoas
43	chr10:97309600-97313800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr10:97309800-97310800	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr10:97309800-97311000	Enhancers	Gastric	stomach
46	chr10:97309800-97311200	Enhancers	Brain Cingulate Gyrus	brain
47	chr10:97309800-97311400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr10:97309800-97311600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr10:97310000-97310800	Enhancers	Lung	lung
50	chr10:97310000-97310800	Enhancers	Ovary	ovary

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