Variant report

Variant	rs11096656
Chromosome Location	chr2:20499761-20499762
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20498204..20500485-chr2:20550867..20552472,2	K562	blood:
2	chr2:20496513..20498388-chr2:20499251..20501283,2	MCF-7	breast:
3	chr2:20326769..20329313-chr2:20498796..20501273,2	K562	blood:
4	chr2:20489518..20491306-chr2:20498308..20500639,2	MCF-7	breast:
5	chr2:20494958..20496619-chr2:20499621..20501776,2	MCF-7	breast:
6	chr2:20488466..20491101-chr2:20497992..20500712,2	K562	blood:
7	chr2:20490728..20492499-chr2:20498984..20500498,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055917	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1043419	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs11096657	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2058553	0.92[ASN][1000 genomes]
rs2160071	0.92[ASN][1000 genomes]
rs4465730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666300	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666379	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]
rs4666384	0.85[ASN][1000 genomes]
rs4666385	0.88[ASN][1000 genomes]
rs62124605	0.92[ASN][1000 genomes]
rs62124607	0.85[ASN][1000 genomes]
rs6531227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706872	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734686	0.95[CEU][hapmap]
rs6741559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579477	1.00[ASW][hapmap]
rs7596183	0.82[ASN][1000 genomes]
rs7606633	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917904	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs989982	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524207	chr2:20448561-20503436	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv999153	chr2:20467929-20521954	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1005366	chr2:20478859-20542134	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11096656	GDF7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20460200-20528600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:20465600-20500400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:20466000-20530400	Strong transcription	Fetal Thymus	thymus
4	chr2:20467000-20522400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:20467200-20526200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:20471800-20522600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:20471800-20533800	Strong transcription	Dnd41	blood
8	chr2:20474600-20528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:20475400-20522400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:20476200-20514400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:20476400-20500000	Strong transcription	Placenta	Placenta
12	chr2:20476400-20521000	Strong transcription	Fetal Intestine Large	intestine
13	chr2:20476600-20500600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:20476600-20516400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:20476600-20524800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:20476600-20526600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:20476800-20516800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr2:20478600-20516600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:20480400-20515400	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr2:20483200-20520200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr2:20483400-20505800	Weak transcription	Brain Substantia Nigra	brain
22	chr2:20483400-20514400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:20485000-20502600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:20486000-20502600	Weak transcription	Fetal Brain Male	brain
25	chr2:20486600-20500400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:20488200-20516400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:20488400-20513200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:20488400-20516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:20488400-20517000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:20489200-20503000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:20489200-20505600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:20489200-20506200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:20489400-20513000	Weak transcription	Stomach Mucosa	stomach
34	chr2:20489400-20517400	Weak transcription	Psoas Muscle	Psoas
35	chr2:20489800-20525800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:20491000-20513400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:20491400-20502600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:20491400-20504000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:20491400-20522600	Strong transcription	HepG2	liver
40	chr2:20491600-20500600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:20491600-20513200	Weak transcription	Brain Angular Gyrus	brain
42	chr2:20491800-20501400	Weak transcription	HSMMtube	muscle
43	chr2:20491800-20513600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:20491800-20514800	Weak transcription	Gastric	stomach
45	chr2:20492000-20502600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:20492000-20505000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:20492000-20506800	Weak transcription	Right Atrium	heart
48	chr2:20492400-20499800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:20492400-20505600	Weak transcription	Esophagus	oesophagus
50	chr2:20492400-20513200	Weak transcription	Aorta	Aorta

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