Variant report

Variant	rs6947441
Chromosome Location	chr7:66162757-66162758
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66149593..66151566-chr7:66161338..66163693,2	K562	blood:
2	chr7:66159384..66161145-chr7:66162392..66164201,2	K562	blood:
3	chr7:66161177..66163221-chr7:66202677..66204246,2	MCF-7	breast:
4	chr7:66161961..66163961-chr7:66193287..66195018,2	K562	blood:
5	chr7:66146126..66147772-chr7:66161839..66164280,2	K562	blood:

Variant related genes	Relation type
ENSG00000154710	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10950047	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11763224	0.81[EUR][1000 genomes]
rs11766583	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12666079	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12667394	0.90[ASN][1000 genomes]
rs1267814	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13311962	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1638724	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1638725	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1638728	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1638732	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1638735	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796212	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796217	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796218	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796219	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796222	0.84[EUR][1000 genomes]
rs1796226	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796227	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862085	0.82[EUR][1000 genomes]
rs1922722	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052089	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420612	0.85[EUR][1000 genomes]
rs2533282	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2533283	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533284	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2707851	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28425729	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28817617	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2901267	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4718364	0.84[EUR][1000 genomes]
rs4718385	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6460311	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6961853	0.84[EUR][1000 genomes]
rs6966953	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6970767	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6979167	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73139927	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73139974	0.81[AMR][1000 genomes]
rs73152714	0.84[EUR][1000 genomes]
rs73377549	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73377594	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801199	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801210	0.91[EUR][1000 genomes]
rs801212	0.91[EUR][1000 genomes]
rs801213	0.91[EUR][1000 genomes]
rs964971	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6947441	GS1-124K5.4	cis	Stomach	GTEx
rs6947441	GS1-124K5.4	cis	Artery Aorta	GTEx
rs6947441	GS1-124K5.11	cis	Thyroid	GTEx
rs6947441	GTF2IRD1P1	cis	Thyroid	GTEx
rs6947441	RP4-756H11.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66148000-66165600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:66148000-66177600	Weak transcription	Aorta	Aorta
3	chr7:66148200-66175600	Weak transcription	Primary B cells from cord blood	blood
4	chr7:66148400-66178400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:66148400-66182400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr7:66148400-66184400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:66148400-66184800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:66148600-66172400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:66148600-66177400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr7:66149000-66177600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:66149000-66199600	Weak transcription	Thymus	Thymus
12	chr7:66149600-66178400	Weak transcription	GM12878-XiMat	blood
13	chr7:66149600-66190200	Weak transcription	Hela-S3	cervix
14	chr7:66151400-66178400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:66153400-66178400	Weak transcription	Fetal Kidney	kidney
16	chr7:66153400-66182200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:66153600-66172200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:66153600-66174200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:66153800-66167800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr7:66154000-66172600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr7:66154200-66172400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:66154200-66177400	Weak transcription	Fetal Intestine Large	intestine
23	chr7:66155200-66178400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:66158000-66177200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr7:66158400-66165200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:66158800-66170200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:66159000-66180000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr7:66159200-66175400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:66159400-66165400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:66159400-66180000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:66159600-66166200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:66159600-66172600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:66159600-66178000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:66159600-66178400	Weak transcription	Primary T cells from cord blood	blood
35	chr7:66159600-66190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:66159800-66177800	Weak transcription	HSMMtube	muscle
37	chr7:66159800-66180800	Weak transcription	Brain Germinal Matrix	brain
38	chr7:66160000-66165000	Weak transcription	Lung	lung
39	chr7:66160000-66177400	Weak transcription	Liver	Liver
40	chr7:66160200-66172600	Weak transcription	Fetal Lung	lung
41	chr7:66160400-66163400	Enhancers	NHDF-Ad	bronchial
42	chr7:66160600-66172400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:66160800-66163000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:66161200-66166000	Weak transcription	Fetal Intestine Small	intestine
45	chr7:66161600-66162800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr7:66161600-66163000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:66161600-66163400	Enhancers	Fetal Muscle Trunk	muscle
48	chr7:66161600-66163400	Enhancers	Fetal Muscle Leg	muscle
49	chr7:66161600-66163400	Enhancers	Stomach Smooth Muscle	stomach
50	chr7:66161800-66162800	Enhancers	Muscle Satellite Cultured Cells	--

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