Variant report

Variant	rs6976879
Chromosome Location	chr7:128327374-128327375
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128320147..128324613-chr7:128325598..128330219,5	K562	blood:
2	chr7:128325647..128328540-chr7:128329512..128331138,2	MCF-7	breast:
3	chr7:128311765..128313824-chr7:128325788..128328720,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM71F2-3	chr7:128327342-128327926	ENSG00000270810.1

Variant related genes	Relation type
ENSG00000205085	Chromatin interaction
ENSG00000271344	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10085435	0.81[EUR][1000 genomes]
rs10224862	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233059	0.82[EUR][1000 genomes]
rs10241185	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10242806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253131	0.84[EUR][1000 genomes]
rs10259359	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10270431	0.84[EUR][1000 genomes]
rs10270985	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10274878	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10276810	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10954205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11761312	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766319	0.86[AMR][1000 genomes]
rs11768485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12333625	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12535238	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536288	0.89[ASN][1000 genomes]
rs12706858	1.00[ASN][1000 genomes]
rs13224613	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13233377	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235219	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13237593	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521711	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs339070	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs339071	1.00[ASN][1000 genomes]
rs339074	1.00[ASN][1000 genomes]
rs339079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34120723	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34490491	0.84[EUR][1000 genomes]
rs34751214	0.84[EUR][1000 genomes]
rs35247963	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35336068	0.93[AFR][1000 genomes]
rs35825132	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35871589	0.85[EUR][1000 genomes]
rs3816421	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4289745	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6467181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs6467201	0.84[EUR][1000 genomes]
rs6467205	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6943737	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946179	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954329	0.90[AFR][1000 genomes]
rs6960296	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6961754	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6967393	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6971819	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6972787	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71548762	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776915	0.81[EUR][1000 genomes]
rs7778731	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7787764	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7790478	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7794447	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs7804472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7810047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9690934	0.84[EUR][1000 genomes]
rs9692416	0.84[EUR][1000 genomes]
rs9768808	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9769753	0.84[EUR][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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv966738	chr7:128325654-128339129	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6976879	RP11-274B21.10	cis	Skin Sun Exposed Lower leg	GTEx
rs6976879	CICP14	cis	Muscle Skeletal	GTEx
rs6976879	CICP14	cis	Thyroid	GTEx
rs6976879	RP11-274B21.10	cis	Thyroid	GTEx
rs6976879	CICP14	cis	Esophagus Muscularis	GTEx
rs6976879	RP11-274B21.10	cis	Nerve Tibial	GTEx
rs6976879	CICP14	cis	lung	GTEx
rs6976879	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs6976879	RP11-274B21.10	cis	Esophagus Muscularis	GTEx
rs6976879	RP11-274B21.10	cis	Esophagus Mucosa	GTEx
rs6976879	CICP14	cis	Nerve Tibial	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128294800-128328000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:128298600-128329200	Weak transcription	Pancreas	Pancrea
3	chr7:128302400-128337200	Weak transcription	Gastric	stomach
4	chr7:128302600-128327800	Weak transcription	Placenta	Placenta
5	chr7:128310000-128329400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:128311600-128327800	Weak transcription	Brain Substantia Nigra	brain
7	chr7:128313400-128329400	Weak transcription	Esophagus	oesophagus
8	chr7:128313400-128331200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:128313600-128327600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:128313600-128337200	Weak transcription	Right Atrium	heart
11	chr7:128318200-128327600	Weak transcription	NHEK	skin
12	chr7:128318200-128328000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:128319400-128328000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:128319800-128328000	Weak transcription	Fetal Intestine Small	intestine
15	chr7:128320200-128332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:128320200-128337200	Weak transcription	NHLF	lung
17	chr7:128320400-128331000	Weak transcription	Brain Angular Gyrus	brain
18	chr7:128320400-128331000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:128320800-128329400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:128321000-128332000	Weak transcription	Fetal Brain Male	brain
21	chr7:128321800-128328000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:128322000-128328000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr7:128322200-128328800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:128322200-128333000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr7:128322600-128328800	Weak transcription	Brain Germinal Matrix	brain
26	chr7:128323400-128327600	Weak transcription	HSMMtube	muscle
27	chr7:128323400-128337200	Weak transcription	Left Ventricle	heart
28	chr7:128324200-128337200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr7:128324400-128330200	Weak transcription	Fetal Muscle Leg	muscle
30	chr7:128324400-128330600	Weak transcription	Osteobl	bone
31	chr7:128324400-128337200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:128324600-128330800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:128324800-128330800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr7:128325600-128327400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:128325600-128329000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr7:128325600-128330000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:128325600-128330000	Weak transcription	Fetal Stomach	stomach
38	chr7:128325600-128333800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:128325600-128337000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:128325800-128327600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:128325800-128329200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr7:128325800-128330200	Weak transcription	Ovary	ovary
43	chr7:128326000-128328200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:128326000-128329200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:128326000-128330600	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:128326000-128337200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:128326400-128328000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:128326400-128328000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:128326400-128328000	Strong transcription	NH-A	brain
50	chr7:128326600-128329200	Weak transcription	Adipose Nuclei	Adipose

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