Variant report

Variant	rs6961754
Chromosome Location	chr7:128312245-128312246
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	POLR2A	chr7:128311889-128314146	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:128312018-128312282	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:128311980-128313921	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:128311065..128312727-chr7:128337751..128339462,2	K562	blood:
2	chr7:128311765..128313824-chr7:128325788..128328720,2	K562	blood:
3	chr7:128306825..128310882-chr7:128311566..128316462,4	MCF-7	breast:

Variant related genes	Relation type
FAM71F2	TF binding region
ENSG00000241493	TF binding region
ENSG00000241493	Chromatin interaction
ENSG00000270810	Chromatin interaction
ENSG00000252866	Chromatin interaction
ENSG00000271553	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10085435	0.84[EUR][1000 genomes]
rs10224862	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10227608	0.81[EUR][1000 genomes]
rs10233059	0.85[EUR][1000 genomes]
rs10241185	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10242806	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10250369	0.80[EUR][1000 genomes]
rs10253131	0.88[EUR][1000 genomes]
rs10259359	0.83[EUR][1000 genomes]
rs10270431	0.88[EUR][1000 genomes]
rs10270985	0.91[EUR][1000 genomes]
rs10274878	0.87[EUR][1000 genomes]
rs10276810	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10954205	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11761312	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11768485	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12333625	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12530672	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs12535238	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12536288	0.95[ASN][1000 genomes]
rs12537208	0.80[EUR][1000 genomes]
rs12706858	0.84[ASN][1000 genomes]
rs13224613	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13233377	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13235219	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13237593	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13246302	0.81[EUR][1000 genomes]
rs28496126	0.81[EUR][1000 genomes]
rs28521260	0.81[EUR][1000 genomes]
rs28521711	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs339070	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs339071	0.84[ASN][1000 genomes]
rs339074	0.84[ASN][1000 genomes]
rs339079	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs339093	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34120723	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34490491	0.88[EUR][1000 genomes]
rs34751214	0.88[EUR][1000 genomes]
rs34942906	0.84[ASN][1000 genomes]
rs34960471	0.85[ASN][1000 genomes]
rs35247963	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs35336068	0.83[AFR][1000 genomes]
rs35603038	0.84[ASN][1000 genomes]
rs35825132	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35871589	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3816421	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4289745	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55953818	0.81[EUR][1000 genomes]
rs6467181	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6467184	0.81[EUR][1000 genomes]
rs6467201	0.88[EUR][1000 genomes]
rs6467205	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6943737	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6946179	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6954329	0.80[AFR][1000 genomes]
rs6960296	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6967393	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6971819	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6972787	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6976879	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]
rs6977126	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]
rs71546786	0.81[EUR][1000 genomes]
rs71546790	0.84[ASN][1000 genomes]
rs71548762	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7776915	0.84[EUR][1000 genomes]
rs7777625	0.81[EUR][1000 genomes]
rs7778169	0.83[EUR][1000 genomes]
rs7778731	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7787764	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7790478	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7794447	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7798172	0.81[EUR][1000 genomes]
rs7804472	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7810047	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7811083	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9690934	0.88[EUR][1000 genomes]
rs9692416	0.88[EUR][1000 genomes]
rs9768808	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9769753	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6961754	RP11-274B21.10	cis	Thyroid	GTEx
rs6961754	CICP14	cis	Artery Tibial	GTEx
rs6961754	CICP14	cis	Muscle Skeletal	GTEx
rs6961754	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs6961754	CICP14	cis	Thyroid	GTEx
rs6961754	RP11-274B21.10	cis	Esophagus Muscularis	GTEx
rs6961754	CICP14	cis	Nerve Tibial	GTEx
rs6961754	CICP14	cis	lung	GTEx
rs6961754	RP11-274B21.10	cis	Skin Sun Exposed Lower leg	GTEx
rs6961754	RP11-274B21.10	cis	Nerve Tibial	GTEx
rs6961754	CICP14	cis	Esophagus Muscularis	GTEx
rs6961754	RP11-274B21.10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128249600-128319600	Weak transcription	NHLF	lung
2	chr7:128282400-128312400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr7:128284200-128313200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:128284400-128313200	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:128294000-128313200	Weak transcription	Brain Germinal Matrix	brain
6	chr7:128294800-128328000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:128295000-128319800	Weak transcription	Left Ventricle	heart
8	chr7:128295000-128319800	Weak transcription	Right Ventricle	heart
9	chr7:128295000-128325200	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:128295400-128325400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:128298600-128329200	Weak transcription	Pancreas	Pancrea
12	chr7:128300200-128313200	Weak transcription	Right Atrium	heart
13	chr7:128302200-128318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:128302400-128319800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:128302400-128323200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:128302400-128323200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:128302400-128324000	Weak transcription	Aorta	Aorta
18	chr7:128302400-128337200	Weak transcription	Gastric	stomach
19	chr7:128302600-128312800	Weak transcription	Fetal Stomach	stomach
20	chr7:128302600-128323000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:128302600-128327800	Weak transcription	Placenta	Placenta
22	chr7:128302800-128321800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:128303000-128312800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr7:128303600-128319400	Weak transcription	Fetal Brain Female	brain
25	chr7:128305000-128323000	Weak transcription	NHDF-Ad	bronchial
26	chr7:128305400-128317600	Weak transcription	Osteobl	bone
27	chr7:128307200-128313000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:128308400-128323800	Weak transcription	A549	lung
29	chr7:128309000-128323000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:128310000-128319600	Weak transcription	Adipose Nuclei	Adipose
31	chr7:128310000-128329400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:128310600-128323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:128311000-128313200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:128311200-128318400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:128311200-128319400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:128311200-128327000	Weak transcription	HSMM	muscle
37	chr7:128311400-128313000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:128311600-128327800	Weak transcription	Brain Substantia Nigra	brain
39	chr7:128311800-128313400	Enhancers	Stomach Smooth Muscle	stomach
40	chr7:128312000-128312400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:128312000-128312600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:128312000-128313400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:128312000-128313400	Enhancers	Fetal Muscle Leg	muscle
44	chr7:128312000-128313400	Enhancers	Lung	lung
45	chr7:128312200-128312400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr7:128312200-128312400	Enhancers	Fetal Muscle Trunk	muscle
47	chr7:128312200-128313800	Enhancers	Psoas Muscle	Psoas
48	chr7:128312200-128318200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:128312200-128322800	Weak transcription	Muscle Satellite Cultured Cells	--

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