Variant report

Variant	rs7577636
Chromosome Location	chr2:99337309-99337310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99336480..99339286-chr2:99347871..99349769,2	MCF-7	breast:
2	chr2:99329459..99332003-chr2:99335709..99337859,2	MCF-7	breast:
3	chr2:99334681..99338238-chr2:99344696..99347399,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1016124	0.81[EUR][1000 genomes]
rs10177696	0.88[EUR][1000 genomes]
rs10194177	0.87[EUR][1000 genomes]
rs10196218	0.84[CHB][hapmap];0.87[CHD][hapmap]
rs10199267	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10460485	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10496332	0.81[EUR][1000 genomes]
rs11123747	0.81[EUR][1000 genomes]
rs11123749	0.81[EUR][1000 genomes]
rs12471383	0.81[EUR][1000 genomes]
rs12477450	0.83[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs12615301	0.81[EUR][1000 genomes]
rs12622931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391483	0.81[EUR][1000 genomes]
rs13391794	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13410406	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13428808	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1514916	0.88[EUR][1000 genomes]
rs1913621	0.81[EUR][1000 genomes]
rs28783173	0.81[EUR][1000 genomes]
rs41445250	0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs4851150	0.81[EUR][1000 genomes]
rs4851154	0.81[EUR][1000 genomes]
rs58666702	0.88[EUR][1000 genomes]
rs60024860	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6706340	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6729151	0.83[EUR][1000 genomes]
rs6733957	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6737760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740656	0.83[EUR][1000 genomes]
rs6751196	0.87[EUR][1000 genomes]
rs7420869	0.83[EUR][1000 genomes]
rs7558236	0.81[EUR][1000 genomes]
rs7599792	0.81[EUR][1000 genomes]
rs7601040	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv2841	chr2:99296874-99342362	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv535836	chr2:99329084-99353519	Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535837	chr2:99329084-99358356	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv535838	chr2:99335416-99358356	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7577636	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99326400-99342600	Weak transcription	Adipose Nuclei	Adipose
2	chr2:99326400-99343600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:99326400-99346400	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:99326600-99340000	Weak transcription	Brain Angular Gyrus	brain
5	chr2:99326800-99342600	Weak transcription	Liver	Liver
6	chr2:99326800-99343800	Weak transcription	Small Intestine	intestine
7	chr2:99329600-99339600	Weak transcription	Right Atrium	heart
8	chr2:99331200-99337400	Weak transcription	HUVEC	blood vessel
9	chr2:99333000-99342800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:99333400-99337400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr2:99334000-99339400	Strong transcription	Dnd41	blood
12	chr2:99334200-99343200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:99334400-99339400	Weak transcription	Esophagus	oesophagus
14	chr2:99335200-99343600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:99335200-99346600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:99335400-99342800	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:99335400-99343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:99335600-99339600	Weak transcription	Gastric	stomach
19	chr2:99335600-99343200	Strong transcription	Fetal Thymus	thymus
20	chr2:99335600-99345800	Weak transcription	Right Ventricle	heart
21	chr2:99335800-99339800	Weak transcription	Brain Substantia Nigra	brain
22	chr2:99336200-99337800	ZNF genes & repeats	Fetal Intestine Large	intestine
23	chr2:99336200-99337800	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr2:99336400-99337600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:99336400-99339000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:99336600-99337400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:99336600-99337400	Strong transcription	Brain Hippocampus Middle	brain
28	chr2:99336600-99337600	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr2:99336600-99337600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:99336600-99337600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:99336600-99337600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
32	chr2:99336600-99337800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr2:99336600-99337800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:99336600-99337800	Strong transcription	Fetal Kidney	kidney
35	chr2:99336600-99338000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
36	chr2:99336600-99338600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
37	chr2:99336600-99338800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
38	chr2:99336600-99339000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
39	chr2:99336600-99339000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
40	chr2:99336600-99342200	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr2:99336800-99337400	ZNF genes & repeats	Colonic Mucosa	Colon
42	chr2:99336800-99337400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr2:99336800-99337400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
44	chr2:99336800-99337600	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
45	chr2:99336800-99337600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
46	chr2:99336800-99337600	Strong transcription	Rectal Smooth Muscle	rectum
47	chr2:99336800-99338000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
48	chr2:99336800-99338400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
49	chr2:99336800-99338400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
50	chr2:99336800-99338800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--

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