Variant report

Variant	rs7364
Chromosome Location	chr1:114524661-114524662
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114524656..114527176-chr1:114534209..114536962,2	K562	blood:
2	chr1:114524538..114527431-chr1:114576171..114578316,2	MCF-7	breast:
3	chr1:114523957..114526156-chr16:67217978..67219734,2	MCF-7	breast:
4	chr1:114353109..114354990-chr1:114522325..114525289,2	MCF-7	breast:
5	chr1:114524519..114527329-chr1:114827145..114829580,2	MCF-7	breast:
6	chr1:114523401..114526223-chr1:114556190..114558490,2	MCF-7	breast:
7	chr1:114519994..114522230-chr1:114524239..114526511,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116774	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000179044	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10108	0.94[CHB][hapmap];0.92[CHD][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs10494162	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs10494163	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11102703	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs11102706	0.83[ASN][1000 genomes]
rs11102707	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs11102708	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11102709	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12127377	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12129050	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1503832	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs1553450	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs17852555	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1910485	0.88[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs41302825	0.85[ASN][1000 genomes]
rs6669370	0.88[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs6674384	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs7519860	0.92[CHD][hapmap];0.85[JPT][hapmap]
rs7545300	0.83[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7546851	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs756493	0.81[ASN][1000 genomes]
rs878129	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]

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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7364	SYT6	cis	parietal	SCAN
rs7364	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs7364	PTPN22	cis	parietal	SCAN
rs7364	DCLRE1B	cis	multi-tissue	Pritchard
rs7364	DCLRE1B	cis	lymphoblastoid	seeQTL
rs7364	DENND2C	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114518000-114524800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:114518400-114525600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:114518600-114525200	Weak transcription	Dnd41	blood
4	chr1:114518800-114525200	Weak transcription	GM12878-XiMat	blood
5	chr1:114518800-114525800	Weak transcription	Esophagus	oesophagus
6	chr1:114519000-114525000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:114519800-114527000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:114521600-114526600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr1:114521600-114527000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:114522000-114525000	Weak transcription	Liver	Liver
11	chr1:114522000-114525000	Weak transcription	Stomach Mucosa	stomach
12	chr1:114522200-114524800	Weak transcription	Fetal Thymus	thymus
13	chr1:114522200-114525200	Weak transcription	Hela-S3	cervix
14	chr1:114522200-114525600	Weak transcription	Gastric	stomach
15	chr1:114522200-114525600	Weak transcription	Psoas Muscle	Psoas
16	chr1:114522200-114526000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:114522200-114526200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:114522400-114525000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:114522400-114525000	Weak transcription	HMEC	breast
20	chr1:114522400-114525200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:114522400-114525600	Weak transcription	Right Ventricle	heart
22	chr1:114522400-114527400	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr1:114522600-114524800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:114522800-114525000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:114522800-114525600	Weak transcription	Brain Angular Gyrus	brain
26	chr1:114522800-114526200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:114523000-114524800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
28	chr1:114523000-114525000	Weak transcription	Lung	lung
29	chr1:114523000-114525200	Weak transcription	Spleen	Spleen
30	chr1:114523000-114525400	Weak transcription	Brain Germinal Matrix	brain
31	chr1:114523000-114525400	Weak transcription	Fetal Brain Male	brain
32	chr1:114523000-114525600	Weak transcription	Left Ventricle	heart
33	chr1:114523000-114526200	Weak transcription	Fetal Brain Female	brain
34	chr1:114523000-114526400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:114523000-114526600	Weak transcription	HUVEC	blood vessel
36	chr1:114523200-114525000	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr1:114523200-114525000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:114523200-114525200	Weak transcription	Aorta	Aorta
39	chr1:114523200-114525200	Weak transcription	Brain Anterior Caudate	brain
40	chr1:114523200-114525200	Enhancers	Colonic Mucosa	Colon
41	chr1:114523200-114526000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:114523400-114524800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:114523400-114527200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr1:114523600-114525000	Enhancers	Ovary	ovary
45	chr1:114523600-114525200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:114523600-114525400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:114523800-114526600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:114523800-114526600	Flanking Active TSS	HSMM	muscle
49	chr1:114523800-114534600	Weak transcription	Primary T cells from cord blood	blood
50	chr1:114524000-114524800	Enhancers	Skeletal Muscle Male	skeletal muscle

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