Variant report

Variant	rs1182174
Chromosome Location	chr7:2875420-2875421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2869377..2877481-chr7:2880306..2885399,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1182172	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1182173	0.96[ASN][1000 genomes]
rs1182175	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1182176	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1182177	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182178	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1182179	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1182180	0.99[ASN][1000 genomes]
rs1182181	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1182182	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1182183	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1182184	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1182185	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1182186	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1182187	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182188	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1182189	0.95[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1182190	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1182191	0.94[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1182192	0.92[ASN][1000 genomes]
rs1182193	0.92[ASN][1000 genomes]
rs1182194	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1182195	0.92[ASN][1000 genomes]
rs1182198	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs1182199	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1182207	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1182208	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs1183085	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11973498	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs12700373	0.80[EUR][1000 genomes]
rs13230946	0.80[EUR][1000 genomes]
rs13243214	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1614791	0.85[CEU][hapmap]
rs1636247	0.90[EUR][1000 genomes]
rs1636249	0.84[CEU][hapmap]
rs1636250	0.84[CEU][hapmap]
rs1636255	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs1636264	0.95[CEU][hapmap];0.83[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1639066	0.80[CEU][hapmap]
rs1713919	1.00[CEU][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1713920	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2107964	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2158694	0.95[CEU][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2260230	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2266922	0.90[JPT][hapmap]
rs2527677	0.81[EUR][1000 genomes]
rs2527680	0.83[EUR][1000 genomes]
rs2533870	0.84[CEU][hapmap]
rs2533871	0.80[EUR][1000 genomes]
rs2533877	0.81[EUR][1000 genomes]
rs2533878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2533879	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2533882	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2533884	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644275	0.85[JPT][hapmap]
rs2644281	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2644294	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2644295	0.85[JPT][hapmap]
rs2644296	0.85[JPT][hapmap]
rs2644304	0.96[ASN][1000 genomes]
rs2644309	0.87[EUR][1000 genomes]
rs2644312	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35957220	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs757791	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7783400	0.84[CEU][hapmap]
rs7807978	0.85[JPT][hapmap]
rs798485	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs798486	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs798487	0.86[EUR][1000 genomes]
rs798488	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs798489	0.90[CEU][hapmap]
rs798490	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs798491	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs798492	0.85[JPT][hapmap]
rs798493	0.84[EUR][1000 genomes]
rs798494	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs798495	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs798497	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs798498	0.90[CEU][hapmap]
rs798500	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs798502	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs798511	0.81[EUR][1000 genomes]
rs798518	0.81[CEU][hapmap]
rs798528	0.86[CEU][hapmap]
rs798548	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs798554	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs798556	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs798557	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs960273	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv887313	chr7:2875420-2927120	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv887314	chr7:2875420-2944187	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1182174	GNA12	cis	Artery Tibial	GTEx
rs1182174	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs1182174	GNA12	cis	multi-tissue	Pritchard
rs1182174	LOC392620	cis	multi-tissue	Pritchard
rs1182174		cis	Lymphoblastoid	GTEx
rs1182174	GNA12	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
2	chr7:2861000-2881800	Weak transcription	Colonic Mucosa	Colon
3	chr7:2861200-2877000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr7:2861400-2876600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:2861400-2882200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:2861400-2883000	Weak transcription	Thymus	Thymus
7	chr7:2861800-2882400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:2862200-2882600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:2862800-2882400	Weak transcription	A549	lung
10	chr7:2863000-2878600	Weak transcription	Small Intestine	intestine
11	chr7:2863200-2876600	Weak transcription	HUVEC	blood vessel
12	chr7:2863800-2881600	Weak transcription	HMEC	breast
13	chr7:2864200-2881000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:2864200-2882800	Weak transcription	Esophagus	oesophagus
15	chr7:2864800-2877200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr7:2864800-2878600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:2864800-2881800	Weak transcription	Fetal Thymus	thymus
18	chr7:2865000-2877000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr7:2865000-2882400	Weak transcription	Fetal Kidney	kidney
20	chr7:2865200-2876600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:2865200-2877800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:2865200-2878600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:2865400-2877200	Weak transcription	Fetal Brain Male	brain
24	chr7:2865400-2877200	Weak transcription	Stomach Mucosa	stomach
25	chr7:2865400-2878600	Weak transcription	Brain Substantia Nigra	brain
26	chr7:2865400-2879600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:2865400-2882600	Weak transcription	HSMMtube	muscle
28	chr7:2865600-2880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:2865600-2883000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr7:2865800-2877000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:2867800-2877000	Strong transcription	Fetal Stomach	stomach
32	chr7:2868000-2877000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr7:2868200-2876600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:2868200-2877000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:2868600-2877000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr7:2868800-2876000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:2869200-2875800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:2869200-2876600	Strong transcription	Fetal Muscle Leg	muscle
39	chr7:2869400-2876200	Strong transcription	Primary T cells from cord blood	blood
40	chr7:2869600-2877000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:2870400-2881400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr7:2871000-2878600	Weak transcription	Hela-S3	cervix
43	chr7:2871400-2875600	Strong transcription	Primary hematopoietic stem cells	blood
44	chr7:2871600-2875600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:2871600-2876200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:2871600-2876400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr7:2871800-2877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:2871800-2877600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:2872000-2877200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr7:2872200-2875600	Strong transcription	Monocytes-CD14+_RO01746	blood

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