Variant report

Variant	rs7750641
Chromosome Location	chr6:31129310-31129311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr6:31129030-31131105	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:31129080-31129930	A549	lung:	n/a	n/a
3	POLR2A	chr6:31129133-31130873	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:31128767-31131569	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:31129049-31131566	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:31129159-31130029	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:31129267-31129444	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:31128357-31133697	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr6:31129300-31129570	GM12875	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31127915..31129464-chr6:31137096..31138939,2	K562	blood:
2	chr6:31126958..31132315-chr6:31135299..31140140,6	K562	blood:
3	chr6:31103022..31109591-chr6:31125707..31129394,9	MCF-7	breast:

No data

Variant related genes	Relation type
CCHCR1	TF binding region
ENSG00000204531	Chromatin interaction
ENSG00000204540	Chromatin interaction
ENSG00000238211	Chromatin interaction
ENSG00000204538	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2233980	0.86[EUR][1000 genomes]
rs3094222	0.90[EUR][1000 genomes]
rs3094669	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3094671	0.81[EUR][1000 genomes]
rs3095311	0.81[EUR][1000 genomes]
rs3130557	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130562	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130566	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130985	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3131010	0.85[EUR][1000 genomes]
rs3132541	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3132566	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
15	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
16	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv884138	chr6:31114573-31129707	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Idiopathic membranous nephropathy	21323541	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7750641	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31127200-31131800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:31127200-31140600	Weak transcription	Left Ventricle	heart
3	chr6:31127200-31146800	Weak transcription	Small Intestine	intestine
4	chr6:31127600-31129400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:31127600-31129400	Weak transcription	Gastric	stomach
6	chr6:31127600-31129600	Weak transcription	Fetal Brain Male	brain
7	chr6:31127600-31131800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:31127600-31132600	Weak transcription	Pancreas	Pancrea
9	chr6:31127600-31133000	Weak transcription	Fetal Intestine Large	intestine
10	chr6:31127600-31136600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:31127600-31137000	Weak transcription	Stomach Mucosa	stomach
12	chr6:31127600-31143000	Weak transcription	Right Ventricle	heart
13	chr6:31127600-31147800	Weak transcription	Primary B cells from cord blood	blood
14	chr6:31127600-31148000	Weak transcription	Right Atrium	heart
15	chr6:31127800-31129400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:31127800-31129400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:31127800-31129400	Weak transcription	Colonic Mucosa	Colon
18	chr6:31127800-31129400	Weak transcription	Lung	lung
19	chr6:31127800-31129800	Weak transcription	Adipose Nuclei	Adipose
20	chr6:31127800-31129800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:31127800-31130000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:31127800-31130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:31127800-31130200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:31127800-31130400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:31127800-31130400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:31127800-31130800	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:31127800-31131400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:31127800-31131400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr6:31127800-31131400	Weak transcription	Fetal Kidney	kidney
30	chr6:31127800-31131600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:31127800-31132400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:31127800-31132600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr6:31127800-31132600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:31127800-31132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:31127800-31132800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:31127800-31133000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:31127800-31136400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr6:31127800-31136400	Weak transcription	Primary T cells from cord blood	blood
39	chr6:31127800-31142800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:31127800-31142800	Weak transcription	HSMM	muscle
41	chr6:31127800-31146200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:31127800-31147800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:31127800-31147800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:31127800-31153200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:31128000-31129400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:31128000-31129400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr6:31128000-31129400	Weak transcription	Spleen	Spleen
48	chr6:31128000-31129600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr6:31128000-31129800	Weak transcription	Fetal Lung	lung
50	chr6:31128000-31129800	Weak transcription	Osteobl	bone

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