Variant report

Variant	rs6953541
Chromosome Location	chr7:140059595-140059596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:139875437..139877407-chr7:140058708..140060608,2	K562	blood:
2	chr7:140058577..140060177-chr7:140062840..140065625,2	K562	blood:

Variant related genes	Relation type
ENSG00000157800	Chromatin interaction
ENSG00000006459	Chromatin interaction
ENSG00000260231	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10235190	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763598	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12667471	0.83[ASW][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap]
rs12669654	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12703793	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12703794	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12703796	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12703799	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4341086	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368896	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4448174	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4587251	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62490397	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62490398	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6464710	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6464713	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6970664	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6976805	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7786963	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7796411	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7803606	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][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	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6953541	ZC3HAV1L	cis	parietal	SCAN
rs6953541	NDUFB2	cis	cerebellum	SCAN
rs6953541	OR9A2	cis	cerebellum	SCAN
rs6953541	TRIM2	trans	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140026600-140060600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:140033600-140096000	Weak transcription	Stomach Mucosa	stomach
3	chr7:140034800-140085600	Weak transcription	Psoas Muscle	Psoas
4	chr7:140035000-140074200	Weak transcription	Right Atrium	heart
5	chr7:140035200-140060600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:140038000-140060200	Strong transcription	Primary T cells from cord blood	blood
7	chr7:140038000-140061000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:140038200-140061200	Strong transcription	Fetal Stomach	stomach
9	chr7:140038600-140060400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:140039200-140060400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:140042000-140084800	Weak transcription	Hela-S3	cervix
12	chr7:140043000-140060400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:140046000-140076200	Weak transcription	Right Ventricle	heart
14	chr7:140047600-140084200	Weak transcription	Fetal Brain Male	brain
15	chr7:140047800-140064400	Weak transcription	HMEC	breast
16	chr7:140049200-140060400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:140049200-140090200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:140049600-140060400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:140049600-140061200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr7:140049600-140061200	Strong transcription	Dnd41	blood
21	chr7:140049600-140067800	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:140049600-140076000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:140049600-140078000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:140049600-140078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:140049600-140079400	Weak transcription	Brain Substantia Nigra	brain
26	chr7:140049800-140060000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:140049800-140061000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:140050000-140060000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:140050000-140060400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:140050000-140061000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:140050000-140061000	Strong transcription	Stomach Smooth Muscle	stomach
32	chr7:140050200-140061200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:140050200-140079200	Weak transcription	HUVEC	blood vessel
34	chr7:140051000-140061000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:140051400-140068400	Weak transcription	HSMM	muscle
36	chr7:140051600-140076400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr7:140052600-140075600	Weak transcription	Pancreas	Pancrea
39	chr7:140052800-140079600	Weak transcription	NHDF-Ad	bronchial
40	chr7:140054200-140079800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr7:140054600-140061200	Strong transcription	Fetal Intestine Small	intestine
42	chr7:140054600-140077800	Weak transcription	Brain Angular Gyrus	brain
43	chr7:140054800-140059600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:140055000-140060000	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr7:140055000-140063400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:140055000-140063600	Weak transcription	Fetal Lung	lung
47	chr7:140055000-140068600	Weak transcription	Primary B cells from cord blood	blood
48	chr7:140055000-140068600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr7:140055000-140077800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr7:140055600-140067400	Weak transcription	Brain Inferior Temporal Lobe	brain

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