Variant report

Variant	rs6946062
Chromosome Location	chr7:33083107-33083108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr7:33082888-33083204	HepG2	liver:	n/a	n/a
2	RCOR1	chr7:33083058-33083878	K562	blood:	n/a	n/a
3	GATA1	chr7:33082846-33083637	PBDE	blood:	n/a	chr7:33083399-33083407
4	POLR2A	chr7:33083046-33084222	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:33081540..33084360-chr7:33100773..33103351,2	MCF-7	breast:
2	chr7:33069987..33071672-chr7:33082730..33084291,2	K562	blood:
3	chr7:33077269..33080476-chr7:33081522..33083915,3	K562	blood:
4	chr7:32994741..32998161-chr7:33082430..33085540,3	MCF-7	breast:

Variant related genes	Relation type
NT5C3A	TF binding region
ENSG00000122643	Chromatin interaction
ENSG00000122642	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10251079	0.82[CHD][hapmap]
rs10280692	0.80[CHD][hapmap]
rs12113707	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12672785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4236335	0.83[CHD][hapmap]
rs4454197	0.83[CHD][hapmap]
rs6462446	0.83[CHD][hapmap]
rs66798602	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67595817	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67608094	0.80[AFR][1000 genomes]
rs6963198	0.84[AFR][1000 genomes]
rs6965006	0.85[AFR][1000 genomes]
rs6976301	0.83[EUR][1000 genomes]
rs6976843	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029220	chr7:32921484-33262190	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	esv3478254	chr7:32956181-33133477	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	esv3478255	chr7:32956181-33133477	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv3528603	chr7:32956254-33133429	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	esv3528604	chr7:32956254-33133429	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	esv3366191	chr7:32956659-33134592	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	esv3418466	chr7:32968130-33138898	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv830942	chr7:33048075-33246735	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6946062	BBS9	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33042600-33083200	Weak transcription	Small Intestine	intestine
2	chr7:33055200-33083200	Weak transcription	Fetal Brain Female	brain
3	chr7:33056200-33083200	Weak transcription	Gastric	stomach
4	chr7:33056200-33083200	Weak transcription	Pancreas	Pancrea
5	chr7:33062400-33084000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:33066200-33101600	Weak transcription	Lung	lung
7	chr7:33066800-33100800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:33069600-33083200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:33071200-33099200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:33076200-33093200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:33079800-33083200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:33079800-33083200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:33079800-33083200	Weak transcription	Ovary	ovary
14	chr7:33079800-33083200	Weak transcription	Right Ventricle	heart
15	chr7:33079800-33083400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:33079800-33090000	Weak transcription	Brain Angular Gyrus	brain
17	chr7:33079800-33100200	Weak transcription	Brain Substantia Nigra	brain
18	chr7:33079800-33100800	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:33080200-33093400	Weak transcription	HUVEC	blood vessel
20	chr7:33080600-33083600	Enhancers	Stomach Mucosa	stomach
21	chr7:33080800-33083200	Weak transcription	Left Ventricle	heart
22	chr7:33080800-33083800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr7:33080800-33086000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:33080800-33100600	Weak transcription	HSMM	muscle
25	chr7:33081000-33083200	Enhancers	Fetal Intestine Small	intestine
26	chr7:33081000-33083200	Weak transcription	Psoas Muscle	Psoas
27	chr7:33081000-33083200	Weak transcription	Right Atrium	heart
28	chr7:33081000-33083600	Weak transcription	Colonic Mucosa	Colon
29	chr7:33081000-33083600	Enhancers	Fetal Intestine Large	intestine
30	chr7:33081000-33083800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:33081000-33084400	Weak transcription	Fetal Kidney	kidney
32	chr7:33081000-33084600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:33081000-33087400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:33081000-33087600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr7:33081000-33087600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr7:33081000-33087800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:33081000-33089200	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr7:33081000-33089800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr7:33081000-33089800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:33081000-33089800	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:33081000-33090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:33081000-33093000	Weak transcription	Dnd41	blood
43	chr7:33081000-33100200	Weak transcription	Fetal Stomach	stomach
44	chr7:33081200-33083200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:33081200-33083200	Weak transcription	Adipose Nuclei	Adipose
46	chr7:33081200-33083200	Enhancers	Duodenum Mucosa	Duodenum
47	chr7:33081200-33083200	Weak transcription	Osteobl	bone
48	chr7:33081200-33084200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:33081200-33084600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr7:33081200-33084600	Weak transcription	NHEK	skin

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