Variant report

Variant	rs1182184
Chromosome Location	chr7:2872446-2872447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2726267..2731021-chr7:2868792..2873151,4	MCF-7	breast:
2	chr7:2871491..2874448-chr7:2900692..2903272,2	MCF-7	breast:
3	chr7:2870014..2872603-chr7:2880108..2883747,4	K562	blood:
4	chr7:2811026..2812536-chr7:2872365..2874848,2	MCF-7	breast:
5	chr7:2871109..2874393-chr7:2876005..2877937,3	K562	blood:
6	chr7:2865761..2868437-chr7:2870160..2873131,2	K562	blood:
7	chr7:2869377..2877481-chr7:2880306..2885399,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174945	Chromatin interaction
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1182172	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1182173	0.91[ASN][1000 genomes]
rs1182174	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1182175	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs1182176	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1182177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1182178	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1182179	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1182180	0.95[ASN][1000 genomes]
rs1182181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1182182	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1182183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1182185	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1182186	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1182187	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1182188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1182189	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1182190	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1182191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1182192	0.98[ASN][1000 genomes]
rs1182193	0.98[ASN][1000 genomes]
rs1182194	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1182195	0.98[ASN][1000 genomes]
rs1182198	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1182199	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1182207	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1182208	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1183085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13243214	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1636247	0.89[EUR][1000 genomes]
rs1636255	0.82[EUR][1000 genomes]
rs1636264	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1713919	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1713920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2107964	0.92[EUR][1000 genomes]
rs2158694	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2260230	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2527680	0.82[EUR][1000 genomes]
rs2527684	0.83[JPT][hapmap]
rs2527687	0.83[JPT][hapmap]
rs2533878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533879	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2533882	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2533884	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2644294	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2644304	0.91[ASN][1000 genomes]
rs2644309	0.86[EUR][1000 genomes]
rs2644312	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35957220	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs798485	0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs798486	0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs798487	0.85[EUR][1000 genomes]
rs798488	0.84[EUR][1000 genomes]
rs798490	0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs798491	0.83[EUR][1000 genomes]
rs798493	0.83[EUR][1000 genomes]
rs798494	0.83[EUR][1000 genomes]
rs798495	0.82[EUR][1000 genomes]
rs798497	0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs798500	0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs798502	0.81[EUR][1000 genomes]
rs798548	0.91[JPT][hapmap]
rs798554	0.91[JPT][hapmap]
rs798556	0.91[JPT][hapmap]
rs798557	0.86[JPT][hapmap]
rs960273	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv1019463	chr7:2848448-2881872	Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1182184	GNA12	cis	Nerve Tibial	GTEx
rs1182184	GNA12	cis	multi-tissue	Pritchard
rs1182184	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs1182184	GNA12	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2848800-2874800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
3	chr7:2854000-2874800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:2861000-2881800	Weak transcription	Colonic Mucosa	Colon
5	chr7:2861200-2877000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr7:2861400-2874000	Weak transcription	Dnd41	blood
7	chr7:2861400-2876600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:2861400-2882200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr7:2861400-2883000	Weak transcription	Thymus	Thymus
10	chr7:2861800-2874600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr7:2861800-2882400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:2862200-2882600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:2862800-2882400	Weak transcription	A549	lung
14	chr7:2863000-2878600	Weak transcription	Small Intestine	intestine
15	chr7:2863200-2876600	Weak transcription	HUVEC	blood vessel
16	chr7:2863800-2881600	Weak transcription	HMEC	breast
17	chr7:2864200-2874000	Weak transcription	Adipose Nuclei	Adipose
18	chr7:2864200-2874600	Weak transcription	Fetal Brain Female	brain
19	chr7:2864200-2881000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:2864200-2882800	Weak transcription	Esophagus	oesophagus
21	chr7:2864600-2874400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:2864600-2875000	Weak transcription	Gastric	stomach
23	chr7:2864800-2874600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr7:2864800-2877200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:2864800-2878600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr7:2864800-2881800	Weak transcription	Fetal Thymus	thymus
27	chr7:2865000-2877000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:2865000-2882400	Weak transcription	Fetal Kidney	kidney
29	chr7:2865200-2874400	Weak transcription	GM12878-XiMat	blood
30	chr7:2865200-2876600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr7:2865200-2877800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:2865200-2878600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr7:2865400-2874600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:2865400-2877200	Weak transcription	Fetal Brain Male	brain
35	chr7:2865400-2877200	Weak transcription	Stomach Mucosa	stomach
36	chr7:2865400-2878600	Weak transcription	Brain Substantia Nigra	brain
37	chr7:2865400-2879600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:2865400-2882600	Weak transcription	HSMMtube	muscle
39	chr7:2865600-2874200	Weak transcription	Brain Anterior Caudate	brain
40	chr7:2865600-2880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:2865600-2883000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr7:2865800-2877000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:2867000-2873800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:2867200-2873800	Weak transcription	HSMM	muscle
45	chr7:2867200-2873800	Weak transcription	NH-A	brain
46	chr7:2867200-2874200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr7:2867400-2874000	Weak transcription	Osteobl	bone
48	chr7:2867400-2874200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:2867400-2874400	Weak transcription	NHDF-Ad	bronchial
50	chr7:2867800-2877000	Strong transcription	Fetal Stomach	stomach

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